Same issue here. The only way I could fix it was to use the socketfilterfw executable directly, with sudo privileges, on the command line. You can check out the help information for the executable by running:
sudo /usr/libexec/ApplicationFirewall/socketfilterfw -h
which explains what options are available and their general use.
For a specific example, I was able to then use the --remove <path> option which would be the same as using the "-" button to remove something from the list of individual applications that have individual rules set on them:
sudo /usr/libexec/ApplicationFirewall/socketfilterfw --remove /Applications/Firefox.app