When blowing up multiple entities with a charged creeper (such as multiple wither skeletons, skeletons, zombies, and/or creepers the only head the drops is of the first mob spawned.
how to re-create:

• spawn a creeper, wither skeleton, skeleton, and/or zombie in any order (make sure you know what order)
• spawn a creeper near by, and strike it with lightning
• activate the charged creeper with flitn and steel, and let it kill all the other mobs spawned
• the result should be that the head dropped is that of the first mob you spawned.

EDIT: I tested this again with mobs at different locations instead of at the same location. the results are exactly the same.