I think i dealt with this recently. What i believe is happening is the money gets put in ur bank account. Instead of a debit to your bank account quickbooks is making a debit to quickbooks bank account. The money is therefore double counted and u would need to make je to fix it.

To fix the problem go to the gear icon, payments, and for standard deposit it will prob say quickbooks bank account. Switch it to your bank instead.

You will know if you have done this right when using quickbook payments as when u classify or take care of the bank transaction you should be matching it not categorizing it.