I'm not a big fan of Fire/Spotted either.
She always seemed to get on my nerves with her just being everywhere and getting into every Clan's business. And even though Fire chose Sandstorm, with how often she turned up it seemed like he was still unsure, even after all that time. So…. yeah. Not one of my favorites.
I hated Yellow/Ragged. Raggedstar was abusive to her as far as I could tell. Completely unhealthy relationship, but I think what got me the most is that not one single cat ever calls him out on his crappy behavior. Instead, he's always remembered as being ShadowClan's last good ruler until Blackstar showed up. Ugh!
Not a fan of Grey/Silver either. They both just came off as being really selfish about the whole thing. Silver always came off as being a spoiled brat to me, so I don't know if it's the ship itself or my dislike of the character(s).
I always felt bad for Nightcloud. I wrote this in the old forum: I like to believe that Night was in love with Crow for awhile, and he when he came back to their clan she agreed to be his mate probably hoping that he would love her back over time (although knowing full well he was doing this to prove his loyalty). However, as she realized that wasn't going to happen she realized how foolish she was and just got angry at herself and at Crow, so she took it out on him and everyone else. I also think another thing that makes her really angry is that deep down she still kind of cares about Crow and she wishes she didn't.
I like Grey Wing/Slate, but I do agree it was rushed as heck. Could have worked that in way better. And I like Star Flower and Clear Sky only because they're both horrible cats and deserve each other. Also never got the Blue/Oak thing: after reading BP it seemed it was just a one night stand. They did their thing and never talked again until they got into StarClan, and even then it was business.
There are a few more ships that I'm not a fan of, but none that really just… get to me.