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.
Purpose in the Machine - S3-E2
Continuity mistake: When May is sitting on the couch talking to her father, the candles behind them are not lit for a couple of shots. They are lit when they start talking and when they finish.
Continuity mistake: When the Asgardian bends the knife, he bends the tip up at the very end. When he takes his hand off the knife, the entire front half of the knife is straight. The shot changes again and the knife is bent differently again. (00:24:15)
Continuity mistake: When Simmons is scanning the tree, first she holds the scanner vertically, then the shot changes and instantly she is holding it horizontally. (00:07:50)
Continuity mistake: In the interrogation room, Skye asks "The truth. What are you after?" and Agent Ward replies "World peace." A few seconds after this line, the light on Skye's head and hair keeps appearing/disappearing/changes position. (00:22:25)
Continuity mistake: When Agent Ward goes onto the aircraft to find Agent Fitz and Agent Simmons having an argument, Simmons put a cup of coffee on the desk. It vanishes from the desk a few seconds after she does this. (00:15:40)
Continuity mistake: As Mike watches the news in the cafe, he is seen lowering his head just as the shot from the reverse angle ends. From the following shot in front of him, he is seen lowering his head a second time. (00:11:10)
Continuity mistake: When Ward is in the apartment in Paris, he begins a fight with two people. At a point during this fight, a couch is knocked over and two cushions fall off the couch. The cushions disappear a few seconds later. (00:04:45)
Continuity mistake: In the opening scene where Mike and his kid have a conversation outside a toy store, an explosion comes from the top floor of an apartment building. Just before Mike runs off to go save some of the people from the building, he says "Stay with Bernie" to his kid and Bernie then does this. After he says this and runs off, the kid and Bernie are a good foot away from the toy store. The next shot when Mike shouts "Watch my boy!" to Bernie, the kid and Bernie are a great distance away from the toy store without any time to move. (00:01:20)
Chaos Theory - S3-E7
Revealing mistake: When Lash holds Rosalind over the ledge before dropping her, you can see her legs dangling and swinging in a very non-human way. It's obviously a doll or mannequin with ragdoll legs. Especially when her knees bend backwards to what they are supposed to.
Continuity mistake: The background scenery, with the lighthouse in it, moves from right to left when Shield Agent Mac and his old school friend talk to one of the relocated scientists. However, in the next shot, it runs from left to right, as if they are on a boat. In reality, it shouldn't be moving at all. (00:18:16)
Deliberate mistake: The last season touched on Infinity War happening - this season jumps forwards a year, meaning that we should be one year into the "blip" (or snap), with half the universe missing. But The Team is all together, and the world/universe is utterly unaffected. Largely a byproduct of disagreement between the film and TV sides of Marvel, plus scheduling vagueness meaning they couldn't risk spoiling Endgame if they came back on the air before that was released. But considering the show is 100% part of the MCU, that's a pretty massive contradiction.
Revealing mistake: When Ruby flips her mother (Hale) over in her room, it's obvious that Hale is played by a stunt double.
Continuity mistake: When Fitz is examining Aida's head, Mack hands him a bottle of beer. He sets the beer on the table and the beer magically twists itself about. It isn't much and it's easy to miss. It's only a few centimeters or so. (00:38:30)
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.