Well, the thing with looting an npc, killed with magic is well known, I believe. Or at least I do know, that an npc, killed with darkness (if I remember correctly), was or is not loot-able. However, just try to avoid killing npcs with that spell, you are using. It's not like every spell makes you unable to loot, you might want to concsider arrow glyph, that one works properly for sure.
But as for your experience: did you buy the training for the magical way, you are practicing? If you are killing the rats with 'darkness' for example, the training in dark way has to be bought, or else you wont get practice points by casting the spell. Find a trainer and buy the training until the yellow bar is full green. Only if you have done this you will get XP, just cast the spell until you ranked up, then you can go and buy the training for the next level again.
