Often happens. When we do moderation things we try to privilege the earliest submission of a story but it isn't always possible.
We'll eventually get around to working on a more sophisticated way of handling duplicate submissions, but the simplicity of the current approach (i.e. allow a few reposts if a story hasn't had significant attention yet) has much to commend it.
Perhaps the algorithm could be tweaked so that simply voting on a story pushes it closer towards the top of the homepage.
I always search before submitting, and just upvote an existing story if someone has already submitted it (unless it's a from different source, which may get more traction due to being better written).
