I must be lucky where I live. The major chain pet stores have their stuff segmented properly (no goldfish with anything but their own kind, even if they have three hundred in one tank). And every LFS I've been to in my town is vigilant about their separation - brackish, soft water fish, normal ph, discus in their own tanks, etc. They won't sell you a fish if you don't have a tank large enough. "You're not going to keep a great Dane in a 600sqft studio apartment..."
Just yesterday, I actually overheard a shop owner sharing in the misery with a shopper about the poor condition of the last shipment of angel's they received. He said something to the effect of, "I'm not happy about it, but there's not a lot I can do when I've already purchased them from the supplier. We keep up water conditions here and hopefully they'll improve in the shop so folks are willing to buy them." This same store supplies pH neutral freshwater, brackish, and RO/DI saltwater.
We really don't know where most of the supplied fish come from. Waters from a foreign country? A fish farm on the other side of the country? Local fish farms? My favorite local shop deals with their crappy shipments, and you can see the improvement in their stock even a week later.