Character mistake: When Guile promises to rescue the hostages while on camera with Bison, he makes it a point to mention Charlie by name to reassure him that he wasn't forgotten. Anyone in charge of a major hostage recovery operation would avoid naming a specific hostage unknown to the enemy due to the special focus that the enemy may put on that hostage for further abuse. This was promptly proven when Bison specifically chose Charlie to transform into a beast due to Guile identifying him as a personal friend.
Character mistake: The Matterass twins are playing a video game, and they argue about whether to destroy Milwaukee or Minneapolis. They decide on Milwaukee but destroy Hibbing Minnesota.
Character mistake: After Maverick gives the "actors" their hundred dollars, he says "News travels fast in the Old West." Why would he refer to the west as "old" when, for him, it's the present? This is an expression that didn't come about till later on, when the west BECAME old.
Suggested correction: This was a joke, since it's a comedy movie.
Character mistake: Shiwan Khan uses mind control to make Nelson commit suicide. Later, when Lamont is talking to one of his agents, the agent talks about a murder at the museum.