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: 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)
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)
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.
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 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: 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.
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: 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)
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.
Revealing mistake: When Ruby flips her mother (Hale) over in her room, it's obvious that Hale is played by a stunt double.
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.
Other mistake: The module on the alien spacecraft Fitz repairs, most visible when he says "OK we're done, we're done" is just a standard PC motherboard, which also has no connections to anything else - it's just glued to the metal panel he's holding.
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.
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.