In QuickBooks Self-Employed (QBSE), negative transactions on the Transactions menu are treated as an expense. You can mark them as Business or Personal.
However, if they're not supposed to be an expense, you can exclude these transactions. Then, manually add them with the correct one.
Here's how:
In QBSE, go to the Transactions menu at the left pane.
Locate the transaction you want to exclude and select it to expand the view.