if documents do not show up on your document report, it would indicate that something is wrong with the filter (i.e. your filter is not pulling in the documents that are being uploaded). Are you able to explain why this is the case? Or maybe even post the filter that this report is using?
It also sounds like at some point a decision was made that the only items that should show up on your report are files where you have edited a custom column. Why was this decision made? Did this team specifically start out wanting to exclude some uploaded files, before changing their mind?