When I was 98.9% done downloading a file the amount downloaded began to go backwards. I had 72.2MB done and now it's down to 71.7 but the percentage done hasn't changed at all. How is this possible? More importantly, how do I fix it?

This happens when you have hash verification errors.

You see each chunk has a hash, so we can verify if the data is correct. You need the whole chunk to verify this hash. When a chunk is downloading we add those bytes to the number downloaded. So when we detect that the hash doesn't match, we have to subtract the size of the chunk from the downloaded amount.

You can argue whether this is good, if we were just to add each byte we downloaded, things would be simpeler, but then we would have people complaining that KT downloads more then the size of the torrent.