Where does fruit flies come from?

They might not necessarily be fruit flies but instead could be fungal gnats which are attracted to the decomposition in the fruit. Fruit flies can do a lot of damage to orchards as well as home garden fruit trees which is why many countries quarantine any areas where they are found. The fruit fly will actually be on the fruit at the time you purchase it.

they annoy the hell out of me, we had that problem when there was some potatoes left that had been forgotten about, OMG there was too many to deal with. managed to get rid of them all though by removing the potatoes.

I don't know where they come from, but they always know when there is a fruit laying out somewhere and they'll come and get it.