Factual error: During the 31st year of the Avalon's voyage, the ship passes close to the star Arcturus, which is about 37 light years from Earth. Later in the movie, it was stated that the Avalon was moving at around 50% of the speed of light. The ship would not have reached Arcturus in the time allotted.
Revealing mistake: Just after Aurora finds out that Jim woke her up, she runs around the ship. When she finishes the run, she comes across a dead end and the shot cuts to Jim sitting in front of CCTV monitors. If you look carefully, her movements on the middle monitor do not match the two either side of it - a badly-synced video rather than a live CCTV feed. (01:04:00)
Continuity mistake: In the scene in the bar where Aurora discovers she was woken up, when she walks out and says to Jim "stay away from me" - she points at him initially then spreads open her fingers, but when scene cuts back to Jim a second later you see a single finger pointing.
Factual error: The Avalon generates its gravity by rotating, which is made evident by the fact that the elevators connecting the three helical pods are without gravity. When the passengers go spacewalking, the instant they walk out the airlock, they have to be secured by magnetic boots. When they turn them off, they become weightless. Both assertions are wrong for the same reason: If the gravity is created by centrifugal force, that force is present on all points of the ship with the strength depending on the distance to the hub of the ship, no matter whether that point is inside or outside the ship's hull. That of course includes the ledge in front of the airlock. Any surface that is oriented towards the hub of the ship is felt as "floor", surfaces radially oriented to the hub would feel like "walls", surfaces oriented away from the hub would be "ceilings." So if you step off a ledge on the outside of the ship the way the actors do, you'd be drifting away from the ship on a tangent to the ledge you stepped off, and end up hanging by your tethers. You wouldn't accelerate away from the ship like you would in a real gravity field, but you would float away with a speed equal to the acceleration simulated by the artificial gravity. The only way to become weightless would be to cancel the sideways motion imparted by the rotation of the ship. At the rotation speeds depicted in the movie, that would take at least a motorbike to do.
Plot hole: In multiple scenes in the movie the starship is in a gentle rotation which allows 1G gravity on the ship. When the power to the propellant is cut the rotation stops and gravity is lost. Such a design for a starship doesn't make sense as the entire structure could be put in a continuous motion, as is indeed done with many probes today without requiring the continuous addition of power. Even if this design was chosen with part of the structure fixed and party of it moving around it still seems unlikely that the rotating part would come to a grinding halt within seconds (if it did, the friction of the structure would be huge, requiring enormous levels of energy to keep it moving) The only reason the movie chooses this unlikely design is to integrate the crucial shot of Aurora floating out of the pool when power is first lost.
Suggested correction: There are parts spinning with different speeds and directions. Spinning an entire solid ship wouldn't allow for things like that. Regardless, we can't say which starship designs make sense or not. The ship has a reactor with seemingly endless energy, so powering the rotation is not a problem. The sudden stop is because whatever spins the ship has lost power. If you try to turn an unpowered motor or engine, especially if geared, you will feel resistance because the mechanism is acting as a brake.
Other mistake: When Jim takes his first 'space walk' you can see that every cabin and luxury cabin light is on, but cabin lights come on when occupied, and all but one person are still in hibernation.
Continuity mistake: Near the end when she puts him in the Auto doc his legs are crossed, then straight in the next shot. (01:39:29)
Factual error: During Jim's first spacewalk, while floating, with no gravity, a tear rolls down his cheek.
Suggested correction: He's not in free fall. He's at the end of a tether, held taut by centripetal force. The tear should have fallen "down" into his suit's visor.
Other mistake: People 'sleeping' in the hibernation pods are lying down under force of gravity, connected by their left hand fingers to sensors monitoring them, they're not strapped in or clamped down in any way. So when the gravity was lost for 5+ mins they would have lifted inside the pod, hit the top, probably disconnected from the left hand sensors, and maybe dropped back down awkwardly out of place for a future arm injection. Maybe even triggered an early wake-up procedure of the pod, as perfect equilibrium would be disrupted by getting no data from the sensors.
Continuity mistake: When Aurora is chatting with Arthur in the bar when Jim appears thinking it's Tuesday, when she turns to him she takes her right hand away from her glass of drink, but a second later her hand is back touching her glass, she couldn't have put her hand back there so quickly.
Factual error: The ship supposedly has some sort of artificial gravitational field because there's a light which notifies when the gravity is off. When the gravity turns off, suddenly everything flies off into different directions. If the ship is moving with uniform motion, turning off the gravity will do nothing unless an object is accelerated. Where it moves to depends on the direction of your acceleration.
Plot hole: Gus wakes up and doesn't realise initially that he's seriously ill, although he knows he's not right. When Jim woke he was given a full body scan to check his health minutes after waking, so surely Gus must have had the same scan? When all his medical problems would have been identified. So he'd have known he was very ill minutes after waking.
Suggested correction: Minutes after waking there was nothing wrong with his body yet, his body started to deteriorate rapidly afterwards.
How do you know nothing was wrong with him minutes after waking up?
Because he got a full body scan like you said and nothing came up. The first sign of symptoms he shows is after they enter the bridge (or command center) and he dismisses it as something common. Before that he shows no sign of any medical problems.
That's the mistake here - he should have had a body scan on wake-up. So did he develop multiple medical issues in the pod because his pod function was affected by the central computer being damaged by the asteroid strike? Which would fit as his pod woke him up early, a built in safety feature perhaps so people don't die in their pods? Maybe his pod wasn't working right for 2 years, so slowly damaging his body? So the wake-up body scan should have detected his multiple issues! He couldn't go from healthy to over 600 disorders in a day.
I'm not sure the pods are sensing anything, they're essentially freezers, but without freezing you. The finger connections are not sensing anything from a person in the pod as there's nothing to sense, as people are dormant. It only senses vital signs when people are woken up. So Gus blaming his pod for his medical issues is inaccurate surely? A movie mistake?
The malfunctioning pod caused his medical issues. It keeps them in cryogenic stasis. We don't know exactly how they work of course but it is more than just sensing. Basically the people inside the pods are kept dead, but the pod manages to halt any deterioration of the cells. Imagine that going wrong and the pod isn't able to keep the cells in check. Just like when exposed to high levels of radiation the cells have been damaged but there won't be any signs immediately. Only after a few hours the cells will start to break down.
He developed several severe medical issues after being woken up too early in a pod that was malfunctioning. This is fictional, future technology and we have no idea how it works, but I think its safe to assume that the pod has to keep the entire body in check during cryosleep, and if the pod malfunctions it could cause all kinds of problems, both directly and later on. If it works on a molecular level than no issue can be detected for quite a while before problems start to show, much like with radiation poisoning when cells suddenly and rapidly start dying whilst hours or even days before you feel fine.
Other mistake: Aurora doesn't get an arm injection when she wakes up from hibernation. The device should have been seen retracting (as Jim's did) just before she got the shock to start her heart.
Suggested correction: We also don't see the finger clips going off her fingers. Her pod was cloudy; we see her from the other side of the injection, and it's possible this was just edited out. It could have happened, and we just didn't see it.
Plot hole: Starship Avalon is supposed to be an extremely highly advanced spaceship with capabilities well beyond current technology. Because the pods are supposed to be "fail-safe"/fail-proof, no provisions whatsoever were made to detect a pod failure or sound an alarm - a severe "oversight" for the ingenious people/engineers behind its creation. There apparently are sensors everywhere to automatically activate certain things (e.g, doors, holograms) when a passenger or crew member enters or approaches yet some of the things the holograms said indicated they were preprogrammed to say certain things, even though those things weren't appropriate under the circumstances. For example, soon after Jim entered the room for Learning Group 38, a hologram said, "Hello, passengers. Will you all take a seat." Surely there would be a sensor to detect that all the passengers supposed to be present were or know that almost all were not! The holograms/androids could not respond to some anomalies.
Continuity mistake: Immediately after Jim sends the emergency message back to Earth, we see a long, overhead shot of Jim slowly walking through the Grand Concourse. To Jim's right the doors to Arthur's bar are visible (towards the top of the screen as viewed from the audience). All the doors are closed. The camera then cuts to a close up of Jim as he continues along the Grand Concourse and to Jim's right we can see into the bar and all the doors are now wide open (not in the process of opening, but instantaneously and fully open).
Factual error: Exterior shots of the spaceship show the main thruster/engine running. In outer space, this would cause continuous acceleration meaning that, during the spacewalk, Jim would have been left behind as soon as he let go of the ship.
Suggested correction: Not entirely correct. He will feel two inertial forces: the first is the forward acceleration you mention, and the second is the radial acceleration outward from the center of the ship, as a result of the ship's rotation. So he will be pulled to a balance point between these two forces.
Other mistake: Near the end of the movie, three birds were flying around the room where trees, vines, flower, shrubs, and grass were growing. There is no explanation for where the birds came from, why Jim would revive them from pods (if that's where the first ones were), or why holograms wouldn't detect them. More seriously, where did all the bird droppings (guano) land - without being removed for decades - and how did the uric acid not cause damage/corrosion to the ship? Also, the confined area would be a breeding ground for various possible diseases which could infect the passengers when they came out of their pods. The unplanned introduction of live birds on the spaceship would cause a variety of unintended problems, some deadly.
Deliberate mistake: After Jim completes the awakening protocols, he is shown to his cabin because his door lights up. That's fine if he's the only one there, but he's not supposed to be. Presumably, there would have been hundreds of other people awakened as well, and the ship can't show all of them to their cabins by lighting their doors at the same time. But reviving every passenger separately and showing them to their rooms one at a time seems highly inefficient.
