Hi @Carl_Watson,
Welcome to the forum!
During your processing, did you by chance use robotic extraction or PCR? Do your blanks look more like the samples they're next to?
Well-to-well contamination is a know issue, you might want to look at this paper about it.
If you think its a cross-contamination issue (sample splashing into control), I wouldn't filter based on your negative controls. But, you may also want to check out some of the contaminant filtering threads (these were just the top hits on my search).
EDIT: One more question, what various metrics are showing no difference?
Best,
Justine