It isn't strictly true that there exists only one ISBN per book. Though it wasn't explicitly stated above, hardcovers and softcovers of the same title have different ISBNs. This is a fairly logical thing to presume, but there are other situations where publishers don't exactly play by the rules - books whose cover art has been modified during their runs (movie tie-in covers, book club editions and the like) sometimes have different ISBNs as well.
They shouldn't - generally when the new covers are released the old versions are no longer printed and the ISBNs should transfer from one edition to the next. The only reason to have two separate ISBNs for two practically identical books is if they're both in print at the same time (which would be nice, in my opinion - most people shopping at my bookstore despise tie-in covers with a passion. We wouldn't stock them if we had any choice) but they rarely are.