I can still see a penalty being issued out like maybe you also lose the materia before the one you are trying to add.
ex: you are trying to put you're third materia on but you fail. you lose the third and the second.

or maybe you make it so that a failed materia synth drops the durability down to zero and forcing the player to repair the gear before trying again. in this case you only lose the first materia but need durability of 100% before you can try again