Plot Hole: "In Captain America: Civil War (2016) Tony Stark figures out that Peter Parker is Spider-Man and we’re never told how."

Explanation: "That doesn’t break the rules of the universe, however, since we know that Tony Stark can probably easily access a lot of security footage (he even shows some to Peter) and we can imagine that he used that to track Peter down; or there may be a different explanation, dude’s an Avenger after all. It would be different if, say, that teacher from the maths competition group in Homecoming just knew Peter’s identity, without explanation, because one of the rules of the universe is that Peter keeps his secret identity pretty secret."