The ONLY reason to sync Square to QB would be if you create invoices in Square only and not in QB. Square offers that capability. Syncing Square presumes that you do not already have those entries in QB.

It SHOULD be impossible for a synced Square transaction to exactly MATCH any or a group of transactions entered in QB UNLESS you also entered the Square fees in QB. A deposit of $96.35 in no way can display a green match to a $100 sale entered in QB, unless you deduct the $3.65 fee. But that is why, if entering slaes data in QB to use Undeposited Funds and deduct the fees in the deposit