For me, this happens most often with anime (and/or other indie/non-mainstream-western animation). You'll have a perfectly good beginning and middle, and then... not much of an end.
The examples of this that most readily come to my mind are:
Porco Rosso. There's just no resolution to a bunch of the problems in it (iirc).
Howl's Moving Castle. I felt, at the time, that this could be explained by the fact that it's based on a book, so a lot of the stuff that happened at the end that seemed so far out of left field may be explained by bits that were left out of the book or something. But still.
A movie I can't remember the name of, western, with a very important book and some sort of wolf and it's sort of Celtic or something. Really beautiful animation, but... that ending. Just went... Plthbt.