This has happened too me as well just a short while ago!
Been waiting for a bridge officer with beam overload who was alien (I want to have a bridge crew of same species as my avatar :p) and he also had 3 other ok skills I might use later on.
Commission him and bamb, 4 skills that I have no interest in where there were once 4!
I'm seriously getting sick of this, I've had non-stop problems so far, vastly more than I had in beta and where as in beta is didn't effect the overall experience, its seriously ruining the game for me.
Add to that the fact you get 96 hours head start, minus 8 hours per night for sleep making it really 64 if you're not an insomniac and I've already missed out on 20% of that time because of server issues and the steam mess up and we're not even 50% of the way through!
First time i noticed it was in beta in the tuto: reviewed the 3 BOs, chose one, only to find a different set of skills. That was kinda obvious.
if you pay attention, it actually happens a lot. Often, the BO skills you browse when you accept a mission will not be the same when you turn it in. I even saw a change between two hails (first i observed the BO and chose "exit" then went back to Quinn and the BO had already changed). I even experienced a change in race in beta (a human eng BO 'turned into' an andorian while i was doing the mission to get him).
Same happens with Elsa Mora (BO vendor). The skills in beta did change from time to time from what i've seen.
I'd say it's not unintended. It seems that BOs have a sort of randomness, just as loot is probably randomly generated when you actually open the yellow thing.
I generally don't care anymore about their initial skills because of that (and anyhow i don't get most BO rewards due to the bug).
I spent too much time theorycrafting a BO or skills only to never get that exact BO in the end, if I ever get one.
I just focus on traits (linked to race, those cannot be changed). First stop when I get a BO: power store on earth. 3 times out of 4. The base set of skills is never really optimal anyway.
Had this myself a couple times yesterday & once this morning. Even their Names are different than tha one I accepted from the Quest Reward (i.e., BO was named Deedee & upon accepting she was Jackelyn).