While the filters (Global filters, especially) that are in place on your sheets / dashboards may show up in the filter pane of the extract dialog, you can remove them. Are you saying that you remove a filter (from the Tableau Extract), yet you're not seeing the data you expect?
Sorry but I should have updated this post. I generated new extracts making sure the filters were removed from the extract generation and that appears to have fixed the problem. I had never paid attention to this while generating extracts to that is my mistake. I still need to wait for the automatic extract refresh to occur overnight but I expect that this will work after the automatic refresh as well.