How are you dealing with records in the merge window that aren't actually dups?

Does anyone have code or a process they are willing to share for identifying records that aren't the same and shouldn't show up in the merge window? We stay pretty on top of our merges and we are now at a point where 80% of our suggested merges are records that appear similar but aren't and shouldn't be merged. I would love to have a way to identify these records as not being the same so they stop showing up in the window making it harder to see the actually records that need merged. Any help would be appreciated.

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