[Magus]

For this topic, there are far too many to name... but keeping with anime, the ones that pop into my head immediately are: (WARNING: SPOILERS AHEAD!)
TTGL (Tengen Toppa Gurren Lagann): I think everyone else but me loved the end of that series, but when they killed off a certain character in the last ten minutes of the series... as I say, "It was good, but then they killed ******" (don't want to give away too many spoilers). But at least there is word about possible sequels that may redeem this

Chrono Crusade: If they'd actually managed to kill off the main bad guy, then it would be (almost) perfect

Prism Ark: This one really doesn't count, seeing as how there's definitely room for a possible sequel.. but so far, there's a ton of unanswered questions.

... and from here, it's mostly a case of "the endings were really good, but they weren't truly perfect", in which case i can't really count them as endings I didn't like