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.
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.
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.
Revealing mistake: When the ship temporarily loses all gravity, Aurora, who is swimming, is lifted out of the pool along with the water. Jim is sleeping in his cabin, and he and other objects float into the air. Gus, who is also sleeping in his bed, only has his arms lifted up. His body and the blanket stay completely stationary. He is not strapped into the bed, nor is the blanket tightly wrapped to the bed. When gravity is restored, his arms flop back down.
Factual error: Jim somehow plants a small live tree of about 15 feet in height on the ship's Grand Concourse, meaning that he must have constructed a large container of soil (with irrigation) beneath the bulkhead to accommodate the tree's rootball. This is perhaps feasible, given that Jim is a mechanical engineer, and we see his schematic of the root container drawn on the concourse deck. However, at the end of the film, some 88 years after Jim planted the small tree, the ship's actual crew emerges from hibernation to find a tree of truly gigantic proportions growing on the concourse deck. The tree has easily grown to 70 or more feet in height, which would require an approximately equal amount of space below the bulkhead to accommodate its massive root system. Even if Jim somehow continued expanding the root container to the size of a 7-story building below deck, it's unlikely that he could fill it with millions of pounds of garden soil.