I am currently unable to train Commander Level Skills - they are flagged as Captain level prerequisite.
This means that if I wish to rank to Captain, I have to train up in Lieutenant/Lieutenant Commander subskills until this is fixed - basically, there is no real point unless I feel like filling in missing skill gaps from the first pass through.
This effectively makes being a Commander useless in terms of skill benefits.
Try learning the skills while you're on the ground. I was having trouble learning skills while in a ship, but while in ground missions, on starbases, or on my bridge, I was able to learn them fine as long as I was not in combat.
ret skilling up on the ground or on your bridge it seems to have bypassed the error for me, and i was allowed to train into my Commander abilities but i had to have so many Lt Commander abilities first i dont remember the exact number