My Borg BO is messed up at T3 skills with Engineering Team III and Emergency Power to Shields III.
I have an idea how to reproduce it but I want to wait until I get another BO slot before I try it (I have 8/8 at the moment).
I have a couple theories how it happened:
1. Training the BO with a new skill and putting points into that new skill before it "takes effect,"
2. Training a BO with a Captain trained skill (such as Engineering Team III) and then training them with another Captain trained skill in the same slot.
I don't know if they're related, but both of those issues happened in my situation. I spent points in the new EPtS III skill and after I zoned those points were in Engineering Team II and EPtS III had 1pt.
Fortunately she isn't totally borked, I can still use Engineering Team III. I just had to put her into a different station until I can possibly get it fixed.
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.
That's exactly what happened to me today. Retrained the skills, old skill goes away, new one is there. Put 9 levels into the new skill, save it... bang the old skill appears with those 9 points attached, the new skill appears beneath it with a single point in it.
Also, as someone previously mentioned, as a space skill it moves all the skills along one "rank".