Not really programming but I once had an issue that lasted for months like that: I'm working with a software specific to our industry that generate quotes, sales order and production orders.

For quotes and sales order a PDF can be created and archived in the right folder automatically, or you can use the windows "Print to pdf" printer to do that manually which take closes to a minute for the sales person to create the right folder, with the right name and put the PDF in there with the order number.

The automatic PDF creation fail to include our logo each time and I battled for months with the software company that was telling me that everything is working fine.

Until I looked in the metadata of the PDF the company was sending us, few of the PDFs they were sending is did not have any logo and were created by their software, some had their logo and were created with an external PDF printer.

After I realized they had the same problem internally but were lying about it I just took a day to create a python script running as a service on the server that automatically add the logo on the PDF created and that was it.