When chunks are put together the last 4kb of a piece is compared with the beginning 4kb of the next peice, if they dont match then the smaller of the two is trashed and host it was downloaded from is labeled corrupt.

This feature is there so that when you run the downloaded file it is not messed up. While it is unfortunate that this has to happen it is done to protect the file. Hopefully you do not see this happening all the time.