I don't think its just prequels though.

in film class my professor said "flashbacks never work because not everything will ever line up correctly" and to me prequels are just that, flashbacks. Either you are going to change some of the lore to make it fit, or not everything is going to fit.

However i say it happens with sequels too. The reason being that you end up changing things to go in the direction you want. Maybe someone died, and now is somehow reborn? (Resident Evil) or the bad guy from the entire first game is somehow a guy secretly working on your team? (Metal Gear)

I think if a film franchise is predicted to be more than one movie, then they will work with it. The Amazing Spider-Man for example. (Comic spoiler ahead) They could have went ahead and killed Gwen in this movie, heck there were scenes cut of other people dying, but none of it happened because they decided to do a second.

As for prequels, I think if its exploring something that wasn't explained yet, then go ahead. However if its touching the main lore and could affect the popular movie already there, then don't touch it. Like the example they listed, the original went from being scary and well thought out to who cares all because the lore from the prequel.

I think Star Wars is a good example. It expanded the universe and ADDED to what Luke was, but it never changed who Luke is. Sure the movies are not as well done, but we are talking about writing and storytelling.