Why did two Black Mushrooms spawn in my game?

Up until today's patch (1.0.3), you could lose your staff by dropping it.

The components therefore continue to have a chance to drop, else you'd never be able to replace a lost staff.

I've got half the drops for a second staff just from random luck.

The black mushroom drop location is a random variant of a standard dungeon tile. The game doesn't block it from appearing just because you already have it.

D3 dungeons aren't attached to, or created for, particular players. You can roll a new dungeon, play it for a bit, make it public, and leave when someone else joins, and they could do the same thing. In theory, any number of players could pass through the same dungeon, and some of them might want a mushroom :)