As far as comic books are concerned, there is nothing certain when it comes to the history they present. And that is because, with so many years of storytelling, it is impossible not to mess up the continuity. Or, better yet, in order to bring more impressive stories on the pages, it is impossible to respect this continuity.
So, in the comics, there is the retconning. Basically, the history is changed in order to fit the needs of the new story via an unexpected detail. Thus, whether someone is discovered to have been a clone rather than the actual character, whether an important past event is trivialized, or whatever, the history changes.
Does this happen in the MCU as well? Of course it does. Especially when we are considering the first movies, when the shared universe wasn't outlined just yet. Can they ruin one's movie going experience? No. But they are still there.
So check out the biggest retconning events in the MCU! And watch out - there may be spoilers!