Why would my plumber have installed two drain stubs for a single vanity sink?
The only reasonable explanation I can think of is that he didn't know the height of the vanity he was plumbing for. 

If you try to hook up a sink on a tall vanity (~34" high) and the drain is roughed in for a standard vanity, you'll need an extension for your p-trap, and waste space.

In this situation, I would decide which fits your sink the best and cut-off and cap the other one.

Give him a call and find out for sure.