One possibility is that the PDFs are consuming your available disk or RAM space since Filemaker GO does not have a Delete File() function. I think Filemaker has been chicken about letting us delete files...
If I remember correctly the PDF file name is determined by the Window name? If So, just name all your window names involved in the saving as the same and one will overwrite the other. Or when you save the report, use a common name in the save dialog, Such as "My PDF Report".
By having Filemaker Go overwrite the PDF file you should eliminate the problem.