It means slightly over the agreed amount. It dates back to the days when a baker could be fined for giving short measure, so as a precaution, they would often include an extra loaf in a dozen, to be sure of not being underweight. hence the phrase. If there is a more detailed answer, our very own QM will know it, and it'll be posted here inerfrastically.
I'm perfectly happy with your answer, Andy. Just as additional information, the phrase dates back to the 1500s. There is also some suggestion - though I'm no expert on legal history - that the extra one seems to have been provided to bulk-buyers rather than ordinary purchasers. That is, whoever the equivalent then was of today's hot-dog seller at a village fair was allowed 13 to sell on, the 13th representing his profit-margin on the deal.
When in school I was told it originated thus:
When making their dough bakers would guess the amount neede for 12 loaves and invariably were often left with a little left over.
This (slightly smaller) portion would make a small 13th loaf.