I really liked this movie even with the ending. But for two hours you are just trying to survive with the characters another day or even a minute and then ... SURPRISE!... all the aliens are suddenly dead from infection. Then Tom Cruise goes to his ex's house and everybody is fine. House and neighborhood haven't been touched. Weird, abrupt ending.
Sticking with SciFi movies, I hated the ending of Contact. Stupid. But it is unfair to pick on SciFi movies -- so many end stupidly like the original Independence Day (ok the entire movie sucked, but he downloads a virus to kill the enemy hoards?) and 2001 A Space Odyssey, Interstellar (Matthew McConaughey SciFi pics with crappy endings could probably be its own category)...