Unsure if you're using 1 hotbar or 2 hotbars.
I'm not fully leveled on PCT but I'm not having the same issue.
If it's the amount of buttons you want you can have 2 hotbars up at once on gamepad.
If it's how the PCT job abilities are set up, separate and group what you need for each skill, ie: motifs on 1 wheel, muses on another.