This kind of thing seems to happen more often with TV. Buffy was so bitchy & unlikable in the final season of Buffy the Vampire Slayer, that it made me reexamine the entire series as to whether I ever actually liked her at all. I had a friend who was a big Alias fan but sold all her DVDs once the show ended because she didn't like how the finale left things with Sydney Bristow's mother.
Mortal Kombat: Annihilation pisses me off because they killed of Johnny Cage in the 1st 5 minutes! He was the best character in the entire first movie and they killed him!
Trying to reconcile Highlander 2 with any other aspect of the Highlander franchise, including the original movie, will make your brain explode! (I actually once came up with a unified field theory for the Highlander franchise. It was really lame and had something to do with time travel generating radiation that caused genetic mutations, which was supposed to explain why there were so many more immortals on the TV series than there were in the original movie. It still doesn't fit and I'm not even sure why I bothered trying.)
Indiana Jones & the Kingdom of the Crystal Skull tiptoes into that category for me. It doesn't really ruin the previous 3 movies but it does bring the average of the series way down.
As for the crappy Batman sequels, I think they have such a different look from the Tim Burton movies, that when combined with the cast changes, it's easy to think of Shumacher's efforts as almost an entirely different continuity, just like the later Nolan films.
On topic - I liked "Mortal Kombat" and "Charlie's Angels" well enough, but their sequels (which are two of the worst movies I've ever seen) were so bad that they made me never want to see anything even remotely related to them ever again.
Mortal Kombat: Annihilation pisses me off because they killed of Johnny Cage in the 1st 5 minutes! He was the best character in the entire first movie and they killed him!

The first thing that came to my mind was Highlander 2, but that is an example where it just might be best to ignore the sequel all together as it completely fucked the plot elements of the first.
Trying to reconcile Highlander 2 with any other aspect of the Highlander franchise, including the original movie, will make your brain explode! (I actually once came up with a unified field theory for the Highlander franchise. It was really lame and had something to do with time travel generating radiation that caused genetic mutations, which was supposed to explain why there were so many more immortals on the TV series than there were in the original movie. It still doesn't fit and I'm not even sure why I bothered trying.)
For me personally, I think "Indiana Jones and the Kingdom of the Crystal Skull" comes close to falling into this category. However, I try hard to ignore it and only think about the first three movies. Another example would be what happened to the Batman franchise. "Batman Forever" was bad enough, but "Batman and Robin" almost killed the entire franchise for me. Thank God that Christopher Nolan came along and made "Batman Begins" and "The Dark Knight"!
Indiana Jones & the Kingdom of the Crystal Skull tiptoes into that category for me. It doesn't really ruin the previous 3 movies but it does bring the average of the series way down.
As for the crappy Batman sequels, I think they have such a different look from the Tim Burton movies, that when combined with the cast changes, it's easy to think of Shumacher's efforts as almost an entirely different continuity, just like the later Nolan films.