I didn't come across any bugs, but the game can really fuck you over. So, we all know Boone hates the Khans, and as soon as he joins you he just starts dominating them. Only problem is, they fucking hate you, so you're banished as soon as he starts shooting. But you have to go through the Khans to complete the main mission (at least if you're working with Mr.House) because Caesar has the chip. So, I go and just kill every single Khan in the entire game, because there isn't anything else I can do. So, several big missions are an AUTO FAIL, and I later find out that Caesar had the chip, and his body disappeared. So, I had to load a file from the middle of the game, do it all over, and this time loot his body to find the chip. It'd be nice if, you know, the game warned you that Boone will just start zapping a key cog of the game before he joins you.
That, and the game is OVER once you beat the main quest.