I have like 3 skill points ready to use but I'm not getting the prompt to do anything with them. Is there something that I'm missing. I just started the game and am only level 4. I'm just trying to apply them to the first tier but the game just won't let me. I'm playing on Xbox One, if anyone else has this problem on that platform.

I may be oversimplifying, but make sure to hit square (actually, X on Xbox). Then you can equip it.

Coldstone is correct, to apply the point you have to be highlighting it and then press the X button on xbox one. Then it will ask you to confirm you want to spend that point on it. Then after you do that, you equip it with A.

Ok. I saw the tutorial for it but it wasn't letting me use x or a to allocate points in the slot. I completed some story stuff and then I got the ability to allocate points. Not sure exactly what I did. Maybe it was killing the griffin? Anyway thanks for helping.

@laxbro19: The tutorials are kind of strange as they pop up randomly and lock several options until you have passed the tutorial messages.