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.
Agents of SHIELD (2013)
1 deliberate mistake in Season 6 generally
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.
Maria Hill: What does S.H.I.E.L.D. Stand for, Agent Ward?
Grant Ward: Strategic Homeland Intervention, Enforcement and Logistics Division.
Maria Hill: And what does that mean to you?
Grant Ward: It means someone really wanted our initials to spell out "shield."
More trivia for Agents of SHIELD
Question: Is there any explanation to how Agent Coulson is alive even after Loki killed him in The Avengers?
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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.