Beta fish were kept in tiny cups in which they couldn't move
Since when is this unusual? I've seen Betas in cups since I was a child. They come from tiny stillwater pools...it is their nature to live in this manner. I have had Betas and in researching them it said they do best in small containers without flowing water.

The Petco I go to is always clean and from what I have seen all species are well tended. The rodents are active and in clean cages, Unless of course they are piled up snoozing. The Ferrets are playful and have a nice enclosure for them to live.

The new fish are quarantined until they are determined to be healthy. These tanks are marked 'not for sale'
The only problem I ever encountered was getting a few small snails in my tank from some live plants I bought.

I guess a lot of this depends on the ethics of the store managers and whether they are in the business because they care for pets or for the money.