Are the BO's missing or have you not checked the assignments tab? Many people in game were complaining about missing BO's. I suggested they check the right side of the assignments tab and all of them (all of them) said ohh ****.
The missing BOs is a bug when completing missions. Cryptic is working to fix it. They just don't show up and what most people have missed is you also don't get the skill points only the credits and BO points.
So if the BOs do have Rank III Lt skills than it is time to figure out how to farm BOs in a game with BO bugs...This will be fun.