Maker - Alchemy Skill FAQ and Walkthrough

As I understand it:

Level 1 can only make the three low grade crystals
Level 2 adds the ability to make the three mid grade crystals
Level 3 adds the ability to make the three high grade crystals

Sometimes a crystal will jump a grade though, so even level 1 can occassionally spew out a level 2 crystal if you were going for a high level 1 and it upgrades to a low level 2.

Yeah, this seems to be the case for me too. I get a crystal that's a grade higher than it's supposed to be about 10% of the time.