We do have a small percent of our progressive profiling forms that are filled out with a different email address after the first form is filled out.
I created a smart list with a filled out form filter for a speciific form for all time and the result was 4,876 leads; however the form Statistics for all time show 6,905 filled out form. I then filled out that form and changed the email address to a different address, but the filled out form Statistics did increment by 1. The lower number of leads with form fill events is probably because the leads filled out the form multiple times.
So It doesn't appear that someone changing their email address of a pre-populated form is causing this.
You may want to contact Marketo tech support.