It seems that any counterattack spell or ability cast on another unit will cause the bug. It only happens when the said counterattack kills the enemy. I would guess that the game simply does not end the enemy turn in this case. It may be waiting for his attack to finish.
I've also observed this.
Now, the following anecdote is (ironically) from seanw3's "waiting for next beta" mod, but it might be instructive in debugging this issue. In WFNB, an early weapon, the staff, gives a counterattack. In my case, a darkling something attacked a staff-equipped unit, and the counterattack from the staff killed it. In this case, the counterattack was not given to the unit by a spell or ability, but as a function of the weapon itself. Now I'm sure seanw3 knows a lot more about the XML than I do, and it may be that the way his staff works is not substantially different from a spell or ability. Anyway, the game hung on the dead darkling's turn exactly as described in the OP.
