This one happens on Horizion OS, but not Lakka, Switchroot or possibly older versions of the core which can be found here if you're looking to just play that game: https://buildbot.libretro.com/
If you find time to test an older core, please report back and let us know. Yoshi Story should work on the previous version iirc but I never tested it personally.
But is that the only game you're having issues with? If there's others please share examples as Yoshi Story is the only game with game breaking problems at the moment in my tests of the new Mupen64 Next core.