I have the information you need for possible reasons why your transactions are adjusting, af1991.

QuickBooks Online will depend on what kind of transaction is from the apps connected to it.

For the deposit transactions, I recommend contacting Square Support to help you check what are the adjustments for. They have the resources to assist you.

Moreover, refer to this article about categorizing your Square transactions: Review Square Transactions in QuickBooks Online. 

Please let me know if you have additional concerns regarding the Square app. I'll be here to assist you.