I've got exactly the same issue with my Borg BOFF. I can't use my second T2 power since it classes it as a T3 when I try to use it. Can you use your second one though since they're both already top tier?
In all, she has 5 ground and 3 space powers. The 5th ground power displays as her 4th space power and I can train it, but I cannot use it, neither on ground nor (not surprising) in space.
I also cannot teach her any command space power, she's grayed out and the mouse over displays "replaces an unknown node".
I'm a Captain, and my borg boff is a Commander in rank, so it's not a rank issue, nor a slot one.
I have that aswell. I had the following order on my Boff: Beam overload I, torpedo high yield II and torpedo high yield III. now underneath Beam overload I a new skill appeared, Beam fire at will I, and replaced torpedo high yield III in my skill tab. Its really stupid.
I have this issue as well only not a borg officer and with lt commander skils. It was a skill I trade er in and the one that appears is the old skill. It like the old skil did not erase and it messing up her new skills.
Had a thread on this in beta but there was never any real responce. Was able to talk to a Q and A person in IRC and he said we are pretty much SOL due to the fact that reproducing the bug is very hard.