It is pretty common for stores not to take things like guppies, conivcts, etc simply because they are so prolific. People come to these stores all the time trying to sell them; more than the store can sell. I know it doesn't feel fair, but that's just the way it is, especially if you just have mutt guppies. Not all stores are this way, but alot are. I'd see what the third store has to say and hopefully they'll give you a better offer, but don't get your hopes up.
If you're really wanting to breed something to help support your costs, talk to one of the stores and ask them what they need from a local breeder. There is a good chance that there are some species that are popular sellers that are not readily available to them, or they always come in poor health, etc that they would love to buy from someone local who can be a good supplier.
Petco and Petsmart definitely won't pay you anything for your fish, but many will take them as adoption fish.