Fakin' The Funk first reads the header of the file, which contains (among other things) the total length of the song. Then it scans through the audio frames and calculates the actual song length. If there is a mentionable difference in these two values, the file will be marked as corrupted.
In some cases, this is only a "bug" in the header. In other cases it happens that the song simply stops in the middle of playing.