... and wait for it...
That's what happens when you don't work on a plugin for a long time and resort to copy/pasting from the first other "delete" example you find in your code... which in this case would have been the "Remove *unmanifested* files" which simply ensures the file doesn't get zipped back up again...
Remove unused images will probably have the same issue. I'll push up a new version shortly. At least you have a function in the plugin to complete the job in a second pass in the meantime...
Edit: Remove unused images is fine, it appears only the xpgt files function was affected.