I’ll start with a particularly (in)famous one: Ghost in the Shell 2.0.
Over ten years after the original Ghost in the Shell movie was released, Mamoru Oshii went back to the film and re-worked it, changing the tint of the film from greens and blues to oranges and reds to better match that of Innocence (and possibly to distance it from The Matrix), recasting characters, and redubbing/rewriting several lines. Worst of all, several gorgeous, cel-animated sequences were replaced with shitty mid-2000s CGI renders.
If you’re going to watch this movie (which you absolutely should if you somehow haven't already), stay as far away as possible from the 2.0 version. The original version has been released in bluray in just as good of a quality, and you’re only doing yourself a disservice by watching this disaster of a re-edit.