I did the tower mission - snuck in without altering any enemies until I hacked the console with my specialist. The next turn I moved my spec out and hacked a MEC - and then the tower pulse animation cut-scene started again.
The turn after THAT it told me that the stun wore off on all the enemies - and took 20-30 seconds between each pop-up announcement of the stun condition removal - but except for my hacked MEC none of the enemies acted for the three additional turns it took me to mop-up.
I concluded the mission successfully, and ran further missions without seeing any weird or broken effects, so I think it was just this mission.
It seems like a pretty specific set of conditions to reproduce; were I back in the QA biz I would classify this as above cosmetic, but below serious.
I have a bunch of mods but nothing - I don't think - that affects this. I know there's a way to find a list of installed mods, but I couldn't find it when I searched the forums.... if it matters, and someone can tell me where to look, I'll load all of that.
Otherwise I've got the Steam version, so I imagine I'm running LW2 v1.4.