After today's patch they finally fixed the problem with bridge officers having 2 skills in one tier. However there is a new problem. While they only have one skill per tier now, in my cased, I had already promoted my officer to the rank with the 2 skills, now she has one skill, but cant use it, as if she was never promoted.
Mind you this is a ground skill, and her space skill in the same rank and tier IS usable, as she is the appropriate rank, but the equivalent ground skill is GREYED OUT
I too had this issue, though with a space Skill, After the patch the second skill was gone, but i was able to lvl the remaining skill if i wanted to.
Although i swapped it for something else as the skill they got rid of was the prefered Skill.
I have read others had similar issue to yours and they resolved it by training another skill over top from the BOFF trainer, some reported they could re-trsin the same skill, others reported they 1st had to train a different skill before they could re-train the original.
I had this problem too. I noticed that my Sci officer did not have a 3rd ground ability. When I looked at her skill tab, she had two skills that I could not access. One skill had pips for a Lt Cmdr rank, but I could not use it despite my officer being Lt Cmdr. However the tooltip said "Commander" level ability. The last skill was definitely a Commander level ability with the appropriate pips.
I used another science officer to train my current officer with another Lt Cmdr skill. This proved to be a successful work-around because now my current officer can use this new skill.
I don't know if any of this was intended, but I thought I'd report my experience for review.