Ok, that might explain it. The mission stopped me just short of killing the enemies (it was the War Games mission from DS9). I assumed the ship would get some exp from the mission rewards as well. I guess the thing that concerned me was that it did not give me an number other then 0. I expected to see something like "5439…
There is a liberated borg boff you can get, however it is a pre-order bonus. You get it after selecting your faction according to the post here: http://sto.perfectworld.com/news/?p=877151