I know this is marked "solved" but we are struggling with this issue ourselves.

There are not just hundreds, but THOUSANDS of Deposit Adjustments clogging up our Square App transactions in one client's QBO. 

For two months of activity, it's 98 pages with 25 sales receipts on each page.

This is too many to correct as the OP corrected.

Has this gone away for anyone else with a disconnect and reconnect with Square? 

That's our next step after we untangle having partially processed July so far.