The Bridge - S1-E10
Revealing mistake: Agent Coulson turns the steering wheel several times despite the car being on a straight street.
Purpose in the Machine - S3-E2
Factual error: When examining the sand, Bobbi states "According to carbon dating..." Fitz finishes by saying "It's a billion years older than the earth." However, carbon dating is only good at determining the age of something to about 60,000 years old. The only thing carbon dating could tell about the sand is that it is 60,000 years old or older. It certainly couldn't determine that the sand was 5 billion years old.
Audio problem: Coulson is talking to a cowboy who sold a piece of construction equipment to some bad people. The cowboy pulls a breach-loader shotgun. Ward grabs the weapon and pulls the cowboy off his horse. Next the distinct sound of racking a shell into the breach of a magazine-fed shotgun can be heard, but the breach-loader is seen.
Continuity mistake: When Fitz and his dad are walking together and talking about Dr. Radcliffe, the tablet computer that Fitz' dad is holding jumps from his left hand to his right hand between shots.
The Return - S4-E21
Continuity mistake: During the fight between Coulson, May and the two Ivanovs, the metal pipe that Coulson is wielding gets bent when Ivanov takes it off him. When he throws the pipe to the floor, it's straight again.
Continuity mistake: When Jemma, Skye, and Ward are at the Academy it is daytime. When Seth and Donnie are in the parking garage it is night time briefly. Then, it becomes daytime when they flash back to Ward, and remains daytime when they flash to Seth and Donnie.
Factual error: The image of Faro Portugal seen in episode 10 of season 2 is actually an image of "Ponta Delgada", a city on an island several hundred miles away.
Character mistake: Lance and May walk into a bar in Massachusetts. As they enter, the camera pans and shows a large banner on the front window. The banner is advertising "game day" food and drinks. In very large letters the banner shows Boston Red Socks. The actual correct spelling is Boston Red Sox. (00:05:45)
Continuity mistake: After the interrogation, Skye tells Agent Coulson about Agent Ward. Coulson says during this scene,"It's a magical place" and Skye says "Ward doesn't like your style. Kinda think I do." At The End of this line, Skye is looking at Coulson. In the next shot, she's suddenly looking 90 degrees in the opposite direction. (00:26:55)
Factual error: When Lance Hunter is about to be captured by the military at the beginning of the episode, the troops arrive in a convoy of humvees. The humvees all have Virginia license plates on them, but U.S. Military tactical vehicles do not use license plates. Even if we assume they were using Hummer H1s instead of tactical humvees (commonly used as a substitute on TV and in movies when producers can't get military humvees), military-owned non-tactical vehicles do use license plates, but they don't use state license plates as seen here. Instead, they use official U.S. Government license plates like the ones on the Ford sedan Hunter was dropped off from prior to meeting General Talbot. (00:01:55)
Continuity mistake: When the Chairperson calls the meeting to order and wants to swear in Daisy, you see Senator Nadeer is already sitting next to him. In the next shot, as Daisy is standing up, Nadeer is taking her seat.
Collision Course (Part II) - S6-E9
Continuity mistake: When Mack and Davis slide down the rope, they're wearing gloves. You see Davis take his gloves off, but Mack hasn't quite started to when we see Yo-Yo close to landing. When the shot cuts, Yo-Yo is landing and Mack now has his gloves off as he draws his weapon.
Continuity mistake: When Daisy and May knock on the door of the SHIELD contact, the agent opened the door outward. Later when they were under attack, May dragged the agent in, and Daisy closed the door from inside. (00:17:39)
Other mistake: Sky's dress has no bullet holes, although she was shot twice in the stomach.
Continuity mistake: Right after Yo-Yo runs into Ivanov in the hallway, Fitz fires his gun at the robots. His gun is empty after he fires it. But in the following shot, it's been reloaded again.
Continuity mistake: When Daisy throws Ruby into a tree, her circular blade lands somewhere off-screen. But moments later, it's right next to her.
Continuity mistake: In the scene when Coulson is using a diagram to explain to The Team that Cybertek is the common denominator of everything that's happened during the season, he starts tracing lines that connect various bubbles of the diagram to each other, ending with one that links "the bus" to "GH-325." In the next few shots that last segment suddenly disappears, only to reappear later on. (00:04:15)
Together or Not At All - S5-E7
Continuity mistake: When Faulnak hands the gun to Kasius at The End of their firearms conversation, he turns it around so that he's offering the grip. In the next shot, he's holding it by the grip and offering the barrel instead. (00:16:35)
Continuity mistake: When Daisy is hugging Jemma after proving they're both human, Daisy's right arm is hooked entirely around Jemma's neck. There's an angle change and a lens flare (possibly to help cover the cut) and Daisy's right arm is now at 90°, with her hand on Jemma's left shoulder. (00:21:15)
Continuity mistake: When the Watchdogs destroy the government facility near the start of the episode, 6 shots of Nitramene are fired onto the building's exterior before it implodes. But moments later when Coulson calls Mack, he (Coulson) is watching the news report of the event, and the 6 shots of Nitramene are nowhere to be seen.
Chosen answer: Coulson believes he was resuscitated then sent to Tahiti to recuperate. "A magical place," he calls it. But in the "Agents of S.H.I.E.L.D." episode "The Magical Place", Coulson, through a mind-reading machine, learns that he was treated by S.H.I.E.L.D. and a fake memory of Tahiti was placed as a "mask" of sorts over the painful memory of the operation, which involved a drug seemingly of alien origin to repair the damage, coupled with a lot of morally dubious surgery.