Currently, magic affixes are selected just randomly from a list of available affixes.
But each affix has a frequency. The real issue is that some affixes have a frequency of 0 that means they are not supposed to be picked up (used only in crafting) and not doing so result on an item that can have the Serpent's affix twice (one being of frequency 0 but in a different group).
So the item will have +x Mana twice, because the affix of frequency 0 should not have been picked up.

cc @giviz