I suspect the same that Krum mentioned. Your user was probably logged out when he tried to pay. The pro-form is also a signup form when the person isn't logged in. If he enters his email, then WordPress will say that address is already in use, by him actually.
To make sure that existing users are logged in when they plan to upgrade, it's always best to have the payment pro-form protected with at least Level 0, which will require the person to be logged in and not show it to a visitor. You can do this with conditionals around the pro-form, or just protecting the whole page with the Level 0 restriction.
I hope that makes sense.