Most Magic and some Abilities when picked up from a location in the world (as opposed to shops) will be rewarded to the player in a progressive order to prevent steamrolling the early game with really strong abilities. Buying anything from a shop will give you that exact thing, progression be damned.

You have no black magic. You find Fire2 in a shop and purchase it. You receive Fire2 and can cast it at will as long as you have the requisite ability or the black magic job. Later, you find a chest that in your spoiler log indicates it's the Fire Black Magic Progressive line. You open it and receive Fire 1. Then, you go to Kuzar and find another Fire Black Magic Progressive line in place of Artemis' Bow. You select it and receive Fire3.

*Note: Blue Magic learned through the learning passive ability ignores progression*