He attacked you because you probably provoked him earlier in the game or accidentally stole from him without realizing you did.
The soul gems are in the inventory of a few Mages Guild inventory, alongside being fairly common in dungeon loot at lv. 16+.
Also a note, if something like Ontus attacking you happens again, hold block (LT I believe) and select the character with block still held. This will yield to them, and -usually- make them stop attacking. Now this won't work with people that are normally hostile to your faction, but it works on guards and the such. They'll just ask you to go to jail/resist/pay.
I know about the yield,it said he rejected,and about the factions, he was a mage I think coz of his white robes,I'm a vampire, arch-wizard, fighter's guild master, dark brotherhood listener, madgod, and the gray fox o.o (it was a pain in the ass doing things in the right order so none of the factions would kick me), and about dungeon raids, half of the time those soulgems are filled already T.T
That's pretty crazy... Eh, who cares. I dont like that shop anyways.
I was just asking why it would happen >.>
And I don't care about shops except when I need them