This occurred in version 5.0.4 and 5.0.9, so if it has been corrected in version 6, my apologies for posting to the board.
When I ran bet with the options -m -o -S, I noticed that the overlay was not generated, but the mask was as well as the skull. When I looked at the script, it appears that since bet2 is being called early in this variation, and its outputs to a temp directory, followed by some post-processing steps. While an updated mask after the eye cleanup has been generated, this is not the case for the overlay, and the file is missing. If it would be considerable effort to generate this overlay outside the bet2 executable, perhaps a warning line of text letting people know this won't be generated.