Absolution - S3-E21
Continuity mistake: Fitz drags another agent through the door as it's closing, and one of the Primitives is shown grabbing at the agent's foot, barely missing before it goes through the threshold. Then, in the next shot, suddenly the Primitive is still falling through the air, trying to reach out for the foot that's already inside the door. (00:38:08)
Absolution - S3-E21
Continuity mistake: In the hangar, Simmons unlocks the security door so Fitz can escape the primitives. The control panel changes from a red SHIELD logo reading "RESTRICTED AREA" to blue reading "CLEARED," indicating the door is open. However, moments later while Fitz is fighting the primitives with a fire extinguisher, the door remains open even though the panel shows red and "RESTRICTED" again, then briefly turns blue before switching back to red as it closes. (00:38:03)
Absolution - S3-E21
Continuity mistake: On the security camera, Fitz yells at Simmons that she has a good memory, then asks, "I mean you do, right?" and then he starts to turn to look at the Primatives advancing on him. He's standing up straight, back against the wall with both arms down at his side. Then it jump cuts to a front view of him, and suddenly he's bent over with one hand planted back against the wall. (00:37:45)
Continuity mistake: Hive tells Daisy that he knows she feels bad about lying to Lincoln. She has her head turned to the side, looking up directly at Hive in her close-up. Then, when the angle changes to show Hive, suddenly Daisy is looking straight ahead at her computer screen. (00:31:58)
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.
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)
Continuity mistake: Daisy tells James, "It's not their fault; they don't know any better," and she's looking straight ahead right at him. Then, in the next shot, she's suddenly turned to the side, looking down at the floor while he's responding. (00:14:00)
Continuity mistake: Daisy and James are talking in the bar, and she says she thought Aussies hated American beer. He goes to sit down and says not when it's free, and he is holding his cup in one hand and the pitcher in the other, still holding both as he's sitting down on the bar stool. Then, in the next shot from behind, suddenly his cup and pitcher are already set down on the bar while he's still in the motion of sitting down. (00:13:04)
4,722 Hours - S3-E5
Continuity mistake: When Jemma tells the astronaut, Will, she will be the voice of hope and he the voice of doom. He is looking directly at her after they shake hands. Then, in the next shot, he is looking straight forward away from Jemma. (00:22:45)
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)
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.