I had the same problem. So I placed an NPC contact on a map, I got to speak to the bad guy and the ship looked disabled in the end. What I did was created a big fight right over and around the ship so in the end my BO came on screen and said the Klingon ship is now disabled. It was'nt perfect but it has the right affect. Another trick ... I wanted to beam a hostage off that same ship in the end. You can't interact with the contact like so i placed an anomoly right in the middle of the big fight. My ship actually interacted with the anomoly but in effect, i beamed the hostage off the Klingon ship.