Muxed MPG's and Swarmed Downloads

I have noticed that video in any format will often show artifacts at the "seams" of a swarmed download. Now I have discovered a different problem: QuickTime will read some muxed mpg's (where audio is interleaved with video into one stream) only to the first "seam", though the rest of the data is there. For example, I downloaded a video clip of about 30 MB. In QT, it was under two minutes long. When I ran it through Cleaner, it was 5 min., and when I demuxed it, it turned out to be over eight minutes long.