Actually, I've found that if you accept the bridge officer generated the very first time you open the assignment mission, you do get whatever was generated, and will match what you saw in the assignment screen.
If for any reason, you cancel the assignment screen and reopen, it will randomise the bridge officer again for the assignment screen, and then again after you accept, so what you get will not match the assignment screen.
I believe this to be true from limited testing. I'm alos going to a make a pure guess as to what could be causeing the problem.
IF you accept the bridge officer as soon as the reward is offered no problem.
If you don't accept it and reopen the quest dialog its random and then random again when its assigned to you.
Now here's where I think the problem lies... If you zone or change instances before opening the quest dialog it randomizes the Boff and you're stuck in situation 2 from then on out.
I have experienced this as well. On the majority of officers awarded for leveling. Technically its a quest as its in my starfleet communication just like any of the other quests. But for me I've never had a problem with a mission reward bridge officer only the "bonus" officers I get for leveling.
Additional bugs. If I mouse over a boff don't accept him and then change zones the listed stats will change. if I have 2 or more boffs available to be accepted each time I go back and forth between the two their skills will change.
Once I accept the boff and he is placed in the assignments tab waiting to be accepted or used to train his skills have changed from what was in the quest dialog screen. I have never accepted a boff from anywhere but sector space. Its not that the description changes just a few words, its a total skill change Viral matrix III might change to gravity well II for instance.
In some cases I had 6 and 6 was all I was allowed to have assigned to me. In some cases I had 6 with 8 slots total. in all cases all of my available Boff slots where actually equipped on the ship. (4 seats 4 seats filled) I've experienced this with any where from 2-6 boffs waiting to be assigned to my crew. I find that the most often changed skill is the t4 commander skill. however I have seen all four space skills change to something different from before. I've experienced this in both t2 and t3 with both green and blue boffs.
this has happened with every single boff except twice. in both occasions as I was swapping between two boffs waiting for a skill set I liked (I know I'm sorry I'm abusing a bug, call it for testing purposes) I noticed after about the 3rd or 4th time of opening and closing the dialog the boff skill sets stopped changing and remained fixed no matter how many times I swapped back and forth between my two available rewarded boffs. At that time when I clicked accept the boff that was assigned to me was exactly the same as what was displayed. I have not been able to repeat this reliably.
I have also had the following experience I checked the boffs skill set didn't like it zoned a few times to get it to change and when I finally accepted him his skills reverted to what had originally been displayed the first time I check the reward dialog. I can't be sure about this 100% as I did not pay real close attention and it might have just been random that he was rerolled the exact same way as the first roll.
I have seen this purchasing bridge officers from the bridge officer guy at Sol. I bought the bridge officer for a land-based skill and after purchasing him and choosing to train his skill it was no longer listed. Something else was in the place of it.