A recent update to Notepad++ added color coding that indicates the state of the lines in the file. In the picture below, orange signifies lines that have not been saved:
When I print the file, it gives those lines an orange background:
What setting would I change to disable this feature?
I was able to reproduce this bug with Notepad++ v8.4.6 and had a coloured background (orange and green) like in your picture due to the change process in the printouts or in the PDF.
In the meantime the update Notepad++ v8.4.7 has been released and contains a fix for printing with extra background colors issue due to Change History.
Print to PDF is resulting in: