Hello there, @mortop.
As explained by my colleague EmmaM above, when the invoice payment had bank fees, you'll have to add another line item for it on the transactions. This way, it'll match the amount in your bank feed and avoid any discrepancies upon reconciling.
To resolve this issue, I suggest following the detailed steps shared by RenjolynC above.
If you need assistance with excluding or clearing the transactions, I'd recommend contacting our Phone Support Team. This way, they can help you with this process through screen-share.
Just in case you want to manually upload your bank transactions, feel free to check out this article for more guidance: Manually upload transactions into QuickBooks Online.
Please know you can continue to reach me here with any additional questions. Thanks for coming to the Community, wishing you continued success.
