We have had odd amounts added at the bottom of a deposit that came in from the Square app from any of these items:

--subtractions going to Square savings - these often say "deposit adjustment"

--payments to Square business loans

--other adjustments for refunds, etc.

You might need the Square transfer details report to figure out what the amounts are for. Square doesn't put these "deposit adjustments" in their normal transfer summary or sales reports or transaction reports. 

We've had to use pivot tables with the transfer details report to find how much went to the savings account, how much to business loan, etc. per deposit. 

It's a mess.

Good luck!