I never found this problem before changing to use uTorrent (I think that the selected files should be 100% completed at other peers using other client). So, it usually occured when downloading those torrents created by BitComet (with padding files) (Or no one chooses to download files that 'next to' the files I want) while no peers is using uTorrent. This problem exists if the download has skipped files (also skipped by other peers) but no seed.
I found that some downloads could not be completed using uTorrent, held at ~99.X% (first and/or last pieces of the files were missing).
