Depending on the store and the method of setup, there can be multiple systems. Feeder fish are typically kept in a large tank that has little or no filtration or even, on occasion, circulation, in many stores I see. They are not hooked into the system at all. Some stores do have a few tanks or part of the set up where fish are not in the system, but in a different collection of tanks that share a filter and pump - it is entirely possible that if you have a store that is conciencious enough to bother to observe and wait on selling a fish then they also are smart enough to keep them in separate waters.
The set ups vary widely from store to store. In one of our major pet stores, all the fresh water tanks are joined as are all the salt water tanks. There are "iso" tanks in the back that are not part of the "system" and fish that are deemed "salvagable" are kept there at times. It really kind of depends on what catches the eye of the person who is in charge of the dept. at the time. The other major store has no facilities to quarantine anything!
You have to realize that, from store to store, even in a chain store, conditions vary so widely that you really have to look at each one and how they are run. Some, I am sure are real hotbeds of contamination. Others probably do a fairly good job of keeping things healthy and under control.