Which reports in particular? I'm thinking it's capturing a moment in time, therefore since the lead was once in Marketo and SFDC, it's showing up in the reporting.
I noticed today that my Success Path Analyzer was showing 50k leads 'in flow' for the Lead revenue stage and I know that isn't true. There are only 40k names in our Marketo DB total so it was apparent there was an issue.
What happened is one day last week our SFDC sharing rules went haywire and dumped about 40k leads into Marketo that shouldn't have been there. By default, all new leads end up in the 'Lead' revenue stage once they are deemed 'valid' and enter Marketo. Although they weren't deleted from SFDC (they were deleted in Marketo), they are outside of the Sharing Rule logic so Marketo does not have visibility to these records (anymore).
My guess, as I mentioned earlier, is the reporting is looking at what happened in a specific time period, regardless of what happened to those records moving forward.