In The Amazing Spider-man, Peter's parents leave him with his aunt and uncle at the start of the film. They're never heard from again. Where did they go, what happened to them?
In the film, this is slightly unclear. During a montage, Peter searches for information about Dr. Connors and his parents. This shows that Peter's parents died in a crash. However, later in the film there are two scenes, one where Peter yells at Uncle Ben, another where Dr. Connors is talking to Osborne's henchman, which both make it sound like their disappearance is a secret/mystery. I recall hearing dialogue in one of the trailers that also suggested their vanishing was a mystery.
I'm not the only one to notice this. This article posits that there were some last minute recuts made to the film. As a result, the released version contains hints that Peter's parents' fate is a mystery that Connors and Osborne are involved in.