I too am having issues with the new Connect to Square app.  I just spent 2 hours with support, and was directed to a known issue (INV-72232) where the Connect to Square app is only intermittently pulling in CC transactions from Square.  Some days show cc transactions, others don't.  In my case this has been going on since at least May 9, and making a mess out of my last 2 months of books.  I don't know if anyone can help with this, but thought I would try to make others aware of the issue.