The only real issue I've run across is that of some poor enemy AI. In particular, when I shoot at them from outside their perception, they rarely do anything to prevent themselves from being taken out. This is particularly a problem with Powder Gangers and other lower level gang members, but all types of ants seem to have the same issue. I'll take a pot shot at them which damages them and they basically just stand there doing nothing to take cover or search for who is shooting at them. I'm not even using a silenced weapon - just the varmint rifle with scope. Eventually, after a few shots which hit them, the ants will make a run for me, but by then it is way too late. Ants being silly and just standing there or turning in a small circle wondering what is going on is probably acceptable as they are confused animals... The humans on the other hand should at least seek cover!
Overall this is a pretty small gripe and is not really that big of deal...I just thought the FO3 enemy AI was at least a little better in this instance.