Hi Marcon,
When you receive an online payment, two transactions are generally created. One transaction closes the invoice and is coded to undeposited funds. The other transaction is a spend money transaction that moves the amount from undeposited funds to the nominated bank account when the bank receives it. If both transactions appear in the same bank account, it might be due to incorrectly linked account settings. You can check out this link to troubleshoot your online payment automatic matching.
Thanks,
Genreve