Sometimes a non-valid file is downloaded on a match of one of your filters, even though the name of the torrent is correct. For an example, Chuck.S01E10.torrent matches a filter so it downloads it. But when that download is complete you find out that it's not a real copy of the episode. And if episode 10 isn't going to be released for some weeks time, your feed won't download the real one then if you have "Do not download multiple items with the same season and episode" checked.

How can you remove the download history for a filter? It would be nice to be able to view the download history and be able to delete each individual hit but at this point is there any way currently to get around this?

This is not really possible at the moment, and also not easily done manually.