It's not you, it's eBay. And especially the eBay app, which doesn't allow combined purchases if the buyer uses BIN on each item instead of add to cart. They also prompt payment after a buyer uses BIN on a PC, and in some cases they force immediate payment even if you don't have it enabled.
Unfortunately there's not too much you can do besides guide buyers on apps to use the add to cart function, and / or not to check out until all purchases have been confirmed, and a new invoice issued. Sometimes these tips won't work as the request invoice option can be disabled randomly, but it should hopefully reduce instances of separate purchases and payments.
