If those pages are still ranking in the top 50 for one of the keywords in your campaign, they will continue to be graded. The on-page tool automatically grades pages in the top 50, giving you the opportunity to do a little work to improve a page that is already starting to rank. The fact that they have an F doesn't make any difference to anything.
However, you might not want sub-optimal pages hanging around--you could either redirect them to an appropriate new page (301) or else just 404 them (not found). If you have already done this, it might just need more time for Moz to catch up.
As far as the links, which links do you mean? Sometimes people do link to sites using links with extra, unnecessary characters.