I had the same exact issue - my officer's old ability with the previously allocated officer skill points was visible on my officer's abilities tree. The NEW ability was also visible. There didn't seem to be a way to switch between the two.
I ended up simply re-training the original ability and the 2nd ability disappeared.
I have this same problem. My lieutenant science officer now has two tier 1 abilities (the second ability is the same as the tier 1 ability of my ensign science officer). Due to this, I cannot assign his tier 2 ability to my hotbar (it doesnt show up on the power list although it is shown on the skill tab) and his station shows the tier 1 ability in the tier 2 slot.
I submitted a bug report in game and will try Magnus' fix.
Same thing happened to me just a few hours ago. I tired re training to fix but for some reason I could not get it to work.
Here is what happened (from my original thread)..
So I was adding some SP to my Lt Engineer, and later on while in battle I noticed that my reverse shield polarity power (Lt Power), had been replaced with engineering team (Ensign power). This Boff now has two ensign powers (EM to shields and engineering team) and the reverse shield polarity still shows up but it is unusable now. The thing is, I already have engineering team on my other ensign Boff.
I have gone to the power trainer to see if there was a way to fix this but as of yet I am lost. I might actually have to ditch my cruiser now and try an escort as I now have no other recourse at this time. My Lt engineering Boff is pretty much broken now.
I had some pictures but this sub forum does not allow attachments for some reason it seems.
With the other thred included looks like there are about 6 or 7 of us with the same problem. Bit of an annoyance, but at least my other science officer is fully trained up at lieutenant level now. Still, I'd like my other lieutenants skill to come back