I've noticed that when my Wavewire hacks an opponent, that it only affects his attack skills or pre-battle skills. Reactive skills like 'on ally death debuffs' or 'counter attacks' don't seem to be hacked properly. A prime example is the F9 I hacked during the PvP event that would still weaken my team with his debuff after I killed one of its teammates. However, when it procced on its turn it would attack its own teammates as expected.
Minor but annoying bug.
Another hacking type bug: when a hacked merc with an AOE skill procs and kills itself, the game freezes and you have to shut it down and restart. Any attempt to re-fight that same player will have the EXACT SAME RESULTS and crash the game again.