I think it happened when I went to the Trainer in Sol to buy some new powers but I'm not sure of this. I really don't want to trash this BOFF and restart since I have invested quite a lot of skills into him. I've bug reported this twice with no avail and searched the forums for an answer.
UPDATE: Apparently the t3 Science BOFF power Dampening Field I is actually a Tier 4 power. choosing this power will remove your t3 power and add Dampening Field to your t4, leaving the t3 space empty of anything.