When splitting by payer, Fastoche adds up all payments made by each parent. If there are payments where the parent was not indicated, they will be put on a separate receipt with no parent specified.
When this happens, you can choose to provide the extra receipt to the parents to sort out, or you can resolve the problematic payments. Finding the problematic payments is easy. Simply go to the child, then choose Payments. Each payment made on that account will appear with the payer next to it. You can update the payers and then re-generate the tax receipts.