Not sure that is how alliance works, why are you casting it multiple times? I believe it only applies to the last npc you cast it on. If you cast it on npc A, it improves your faction with that targetted npc's faction, but if you cast it on npc B who is on different faction, it improves that faction but the faction increase to A's faction disappear.
Please correct me if I'm wrong uber enchanters.
Also, casting alliance on yourself makes you like yourself more
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Edit: All that being said, if the npc you were turning the item into con'd amiable right before turn-in, it shouldn't matter. Assuming that quest only requires amiable faction. But if you con'd him, then alliance clicked another npc, it might have changed your faction with the quest npc.