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
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.
Grant Ward: There are two ways we can do this.
Skye: Oh, is one of them the easy way?
Grant Ward: No.
Skye: Oh.
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.