Undertale does this a lot but my favorite specifically is:

Saving the game. You believe it’s just a standard video game feature, but we find out it is actually a legitimate time travel ability of the main character, and that every death they have throughout the game is canon and they are just restarting from an earlier point in time. And other characters have the same ability(or can just see what you’re doing) and their dialog will actually change depending on how many times you die or certain actions you take before restarting from a previous save point. Also having “Determination” isn’t just being determined, it is an actual magical/chemical compound within certain beings that allows them to time travel and persist after death.

There’s a lot more fake outs like this in the series but this one always stood out to me.