I've got a few I can mention.
First off, the Sly Cooper Trilogy on PS3. They're playable, and it might do the job of getting tou in the series, but the games have some audio glitches that just do not exist in the original versions of these three games. If you never played the games, they might not hurt, but the best thing about these ports was that they showed me what the games meant to me if I can see these problems and let them bug me. I'd argue you're better off sticking with the PS2 versions and putting up with their lower resolution.
Then there's the PS2 versions of Sonic Heroes and Shadow the Hedgehog. Say what you will about these two, but these two didn't exactly make the transition to PS2 the best. The ports aren't unplayable, and they were the first time I got to play these, and I had fun, but these are not the best way to experience these titles, if you wanna play them.
I also heard bad things about the Xbox 360 version of Batman: Arkham Origins. The game is glitchy no matter what you play it on, but I was able to get by in the unpatched PS3 version. I suggested the Wii U version to my brother, and he enjoyed it (to this day, he doesn't have a PS3). We both avoided the 360 version, since I heard its glitches made the game darn near unplayable even with patches. Get the PS3 version if you wanna play the game at all.