Same issue here. Though I had all my points spent before. The only ones that had emptied their skill points I had previously spent, were The Performance skills (Starship Engine Performance, Starship Shield Performance, Starship Auxilery Performance, and Starship Weapon Performance)
I'm have the same problem. Each time I use my skill points, the system will not accept the change. Plus, some of the skill points that I had before the latest update were wiped out as though I hadn't spent them in the first place.