I am having the same problem as described by other customer.  Except this seems to happen when a payment performed by bill.com is matched in QBO.  They sometimes show up as a duplicate expense versus a credit against the bill.  I usually have to manually go into the payment in QBO and click "clear payment" to correct.  This is confusing to me and our accountants.  I would like to solve this moving forward.  I can only blame potential synchronization problems or the integration between bill.com and Quickbooks online.