I've also encountered this bug' and have been seeing it with higher and higher frequency. It's not due to recently switching or adding a ship. It happens most often at a map transition. I once encountered it in the middle of doing the neutral zone dailies. I did the sattelite repair mission with bridge officer abilities all present, exited to sector space entered the deuterium supply depot mission and my tray was missing my bridge officer abilities, and my bridge officers were unassigned. I hadn't changed ships or commissioned any new ships, just map transitioned twice.
My theory is that it is either a database corruption problem, or a client/server communication problem. Map transfers have been the cryptic engine's akilles heel since the launch of city of heroes back in 2004. When you enter a map instance, the server sends lots of information to the client. Perhaps the packet with the bridge officer stations is being dropped sometimes.
I always go to space and double check my boff slotting and skills on hot bars before I queue for anything. Especially after ANY change has been made at all. Things you don't think should effect your hotbars sometimes can. I changed out my warpcore and it cleared out all my boffs.
You are Captain of a starship. Never assume everything is going as it should.
I get this as well check bridge officers stations before i start the mission,,,,start mission check again and they have all gone for a coffee......its is a random event for me some times ok some time not and i am lucky in the fact that if i click on a bridge officer station they all reappear,,,,,,,,,