I currently have about 9k skill points earned on my Romulan. I've spent 3k each in ground & space, causing them both to read 'all skill points allocated', leaving me with 3k skill points that the game says can't be spent at all. I know that I'll be able to spend them later, but this may be confusing to new players who aren't entirely familiar with the way STO handles skill points.
Edit: It is in fact possible to spend them if you click on the buttons in despite the UI saying that they're all allocated. UI bug I guess.