Hmm, I'm starting to wonder if this is really true. You didn't use Necropolis's ability to play Fishing Village. In other words, playing Necropolis didn't cause the Fishing Village to be played. Way of the Mouse is what caused it. It's like when you play a Smithy after having played Kiln: The Kiln triggers. You played Smithy but it was the Kiln that caused you to gain another Smithy.
Compare with Enchantress. When you play an Enchanted Necropolis, it's not Necropolis that gives you +1 Card/+1 Action. If it were Necropolis, a Way could still be used. For instance, Way of the Chameleon could replace it with +$1/+1 Action. That doesn't happen, because we're not following Necropolis's ability.
EDIT: Also, the Menagerie rulebook doesn't have this rule. Donald has said it would be included in future rulebooks for BoM, Overlord, Inheritance and Necromancer.