My transaction are listed wrong. Square payments are listed as expenses and some expenses are listed as deposits? How do I fix this?

Good afternoon, canadianfryer-gm.

I appreciate your reaching out to the Community for support. I'd be happy to provide some information.

I recommend undoing the transactions from the banking section to have them fall back into the "For review" tab  by clicking on the Categorized tab > select the items > hit undo tab, then review the settings in Square to make sure the transition goes smoothly. 

In addition, I encourage you to take a look at this article on how to migrate your Square integration in QuickBooks Online. If you require further assistance, you'll need to reach out to the Square support team.

Don't hesitate to reach back out if you have any other questions, Im here to help.