Mainly my problem was with Bob acting OOC and un-Boblike (for example, he's got a weird fangirly moment when he meets DP). He kind of sort of seemed to betray Deadpool, and DP shot him through the hand as punishment (D:). Then there was some kind of cliffhanger with Deadpool writing a letter that said "PS. I killed Bob".
From what I've read, DP was lying and trying to bluff the guy who sent Bob; Bob's not dead and he reappeared later, and continued being a comical sidekick/pet thing. Or so I heard.
But the damage was done, I didn't wanna see stuff like Bob shot through hand :( He's a lot of fun and he was actually the reason why I really fell in love with DP. So I haven't read the current DP after that, and dunno how's Bob doing now.