As title states, the PrepareAnvilEvent fires 3 times. I asked in IRC if this is a known thing, and no one seemed to know, so I'm chalking this up as a bug.

This can be recreated with a simple event that outputs to console and simply place items into and put items out of an anvil inventory:

    @EventHandler
    public void onPrepareAnvil(PrepareAnvilEvent event) {
        System.out.println("Test");
    }