Currently user who have PayPal, or add PayPal and accept invoice payments via PayPal will receive duplicate transactions, one from the invoice itself & the second from PayPal. See screen shot below.
We are working on correcting this. Once we have fixed this, you should no longer receive duplicate transactions. The fix however is forward facing, and will not remove any of the existing duplicates. I would suggest either categorizing them as "Hide Duplicate/wrong income" or simply delete the transactions.
Thank you for your patience & understanding.