Double mortgage payment

I am trying to run an end of the year net cash flow for my taxes. However, I have had my mortgage account in Stessa to basically track the mortgage balance, and I have my rental checking account at a different bank linked for all transactions. So when I make a rental checking payrment via bill pay to send to my mortgage company that transaction shows up and I attached that to my houses portfolio. However, when the mortgage company receives that payment it also shows up as a mortgage payment and so I just attach that to the general portfolio. So when I run the net cash flow for 2020 I show the mortgage payment and a general mortgage payment and so I end up showing a big net operating loss. How do I get rid of the mortgage company receiving the payments from the overall report?