It seems that if an enemy unit is standing on one of their rooms when this room is captured, it is still considered as not in my territory for lightning.
No, this is on a room that originally belongs to the enemy and that I have converted (a very big room, enabling imps to convert it from one side while the enemy units are "busy" fighting my minions on the other side).
I tried with multiple rooms and lightning awas always working after claiming a room with enemy units in it.
Could it be you have misread the situation, eg. you had no mana, you didn't really own the room or just only a part of it but not the part with the enemy units or the units you were targeting are immune to lightning eg. they were prisoners, gold statues, spirits or spirit workers?
No, they were arcanists and priestesses and so. Enemies entering the room but not being on it when it was converted are not immune.
In case this helps : this was with a legacy map (created with v 1.4). I cannot provide a save as saving does not work (see my bug report from today).
Can you verify that this is on a room that you have just lost or before they have finished claiming