I can buy some games with visa gift cards but others I can't, there is cash on card I've already used on this site and it wont let me use it as a payment method.  Is there an option when selling to not allow these cards as payment?

Itch.io has two payments methods:

1. .The developers handle the payments themselves - and I assume there might be developers who only accept one payment method, like PayPal.
2. Itch.io collects the payments on behalf of developers and pays them later. I assume you can buy these games with the Visa card.

It would be nice if Itch.io showed that information on the developer's pages so people know that they're buying straight from the developer or from itch.io - but I don't think that feature currently exists.