Differing doc count with query vs filter

Hi Everyone, we're seeing an issue we don't understand, a differing doc count between a query and filter using a lucene fuzzy search.

There is a detailed explanation on this stackoverflow thread

The basic problem is that a filter using a fuzzy search is giving us a superset of documents that a query is giving us. The explain plans are included in the thread.

Can anyone offer any guidance as to what we're missing?