It is fixed upstream. You just need to update Mupen64plus now and it will work:
1. Press F4 to get to console
2. Type cd RetroPie-Setup
then press enter
3. Type git pull
then press enter
4. Type sudo ./retropie_packages.sh mupen64plus
then press enter
5. Then type emulationstation
and press enter to get back into EmulationStation