Lonely stoppers do appear on ebay.
Given bottles look better with them than without, and they're mostly interchangable because they don't fit, it's perfectly possible to marry them successfully, or swap them between bottles for a more pleasing outcome.
Again, because they don't fit perfectly, it could be fairly random whether a bottle did or did not get a stopper originally.
I personally don't have any "purist" sorts of problems with this.