This is likely to be due to failing to include a reference in the 'Ref' column on the spreadsheet.
Fund Filer relies on references to do its work. Although it uses its own reference system that you never see, it still frets if it doesn’t think you have any. It expects to see them and will just stop if none are present.
It's good practise to get into the habit of having references for your donors. These have to be unique. Fund Filer will ensure this. They are a crucial means of isolating one donor record from another and this can sometimes be vital to a clean and well ordered system with no duplicates.