Seems it's counting trait ability points as core ability points at the moment for the purpose of level up costs (well at least it thinks it is).
ie: One of my mains has 0 points in crafting but is 'Pragmatic' so effectively has 1 point, he just leveled up and has a spare ability point which I'm not allowed to put into crafting, thankfully if I actually have 2 points (quickly grabbed 'All Skilled Up' to check) it does let me level up crafting and it only charges me the 1 point it should cost.
*edit* This also only seems to happen from the controller interface so if anyone else runs into it on PC temporarily switch to mouse and keyboard as a work around ^_^
