Quite by accident I found out that the game for the last several days has not been notifing me when my charactor hits a skill up level. Out of curasotiy I went into my skills window Of my T'Sonie and found 7 k skill points for my commander and over 4k for my officers.
I really do not know how long it took to reach the amoiunt of points I had but I would guess at least 2 days the way I have been playing. I have checked my other 2 charactors and it seems to be affecting them all.
My other Fed charactor, T'Bonee has 17k for the commander, I do believe that for my toons it is broken.