[Sneaky]

I think it has a lot to do with overmedication.
For example, Camallanus nematodes, a once rare and easily treated parasite in tropical fish, now is almost untreatable period. It is immune now to all common antiparasitics, and is only treated with 2 known medicines, Levamisole and Fenbendazole.

If you have been to a commercial fish farm, its easy to note the HUGE mass amounts of drugs fish are treated with. They are dosed nearly daily with antibiotics, anti parasitics, and a wide range of drugs.
Then, the fish get shipped out to pet stores, where they are exposed to even more drugs. Walmart for example, drops a 1 litre pail of antibiotics, antiparasites, slime coat enhancers, and other drugs in each store tank Daily.
Many of these are know to the state of california to cause cancer.
Its no doubt in my mind that the uninhibited use of drugs in aquarium fish has led to many diseases being extremely difficult to treat due to drug resistance, in the exact same way, overmedication of both our meat as its raised and us as humans with illnesses, has led to the development of super bugs.

Combine that with the poor breeding practices you point out, and its a recipe for disaster.