When transferring upgraded weapons to and from containers the + sign disappears making it difficult to tell whether you've got the right weapon or not. It reappears in the PiP inventory if it's still there but it's annoying.
The Dealing with Contreras quests have a couple of bugs; if you successfully persuade Issac to increase supplies with speech (haven't tried with barter) the locations of scrap metal/tin cans still show up as intermediate destinations on the PB. After completely the first two quests and being told to come back the next day, the line "where should I meet Price again" shows up in dialogue even though you've haven't been asked to meet him and the quest hasn't been initiated.