I got this horrible glitch where Batman keeps falling down into an endless pit and I can't get away from it despite my best efforts. It happened right after I finished the game and after completing the Alibi side mission. I checked with an online forum and they told me the best way to fix it is to restart the game in a new slot. Nice.
Honestly, Arkham Origins is a rushed title. There are a lot of bugs in the game and it's definitely not as good as the previous Arkham games. The thing that disappointed me the most was the fighting mechanics. It didn't feel as fluid as it should be. And the storyline didn't satisfy me. Since this is an origin of Batman, I expected some cool backstory of how Bruce Wayne became Batman, how the Joker became Joker - things like that but it didn't happen.
My favorite is still Arkham Asylum.