Had the same thing happen to me. They seem to be tied together. My exact sequence of events:
Purchased the Regent Assault Cruiser Retrofit
Assigned Bridge Officers without a problem
Traveled to another location to have a fleet member train some different skills on one of my officers.
Removed the officer to be trained, stripped his equipment, traded him, received him back with his new abilities.
Upon opening the screen to reslot him, all my officer slots were empty even though I'd only removed this particular one, and only the slot I'd emptied would respond to a new assignment (the officer I'd traded).
Upon returning to space, I found that all the officers that were previously equipped were still equipped, despite the slots showing empty, and all of their abilities were available. The officer I traded for training seems to be working normally, only has his normal set of powers available.
Edit: Game crashed when I attempted to return to it after typing this, upon reloading, the "empty" slots are still functioning as above. Workaround - swap the "empty" slot with an officer that was not originally in that slot, slots return to normal and can be reassigned.
Same sorter thing happened to me with the vesta how i fixed it was by assigning other boffs to tha stations then putting the ones i wonted in the slots. but ive extra boffs on my roster from the zen store. Stupid bugs
I only found I could assign bridge officers when given a new ship or randomly when sto decides I can. But I've found if you buy a shuttle, 40.000 energy for a cheep one. Then assign each officer to that then to you bridge one by one. Seems to wake up the game lol.