Most of the common species are bred in a warmer country i.e. a lot of European fish are bred in Singapore and Malaysia, for the US a lot come out of Florida. They are then boxed up and flown over.
Some other common tropicals, especially some tetras and many catfish are wild caught, and then sent up in much the same way by air.
For some other, more uncommon species, these are bred in 1st world countries such as Germany, the UK and the Czech republic. These tend to be harder to breed, higher value per unit fish such as discus and many African Rift Cichlids, rams, fancy plecs and so on.
There are some interesting articles around this subject on the practical fishkeeping website though you need to dig around a bit.
The amount of fish bred and returned to the shop by the average is pretty trivial really, and only significant in a couple of species that are more rare like Uaru, Zebra plecs, Banggai cardinals