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.
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.
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)
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)
Chaos Theory - S3-E7
Revealing mistake: In the shot where Lash hauls Rosalind over the parapet to later drop her, you can see that he is actually lifting a mannequin as its legs very fluidly bend backwards while it is being dragged over. (00:32:00)
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: 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.
Other mistake: Agents say they have seen seismic activity in South Dakota, but from earlier episodes, Daisy and Lincoln visit South Australia to find out Fire Guy.
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)
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: 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)
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)
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: 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)
Continuity mistake: In the opening of episode 20, Coulson meets General Talbot in a saloon that is a secret entrance to their hidden base, a base that is many stories underground. Yet in episode 22 Coulson uses his robot arm to call another jet; it appears outside a window! He can't have a window in his office, if the base is several stories underground. And to verify it isn't a "video window" or "projection screen", Mac throws a chair through it, essentially saying "We are above ground, let's go get in that jet in front of us." (00:19:40)
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.