This is largely a N64 emulator issue. There is still no good emulator for it because unlike Dolphin, nobody is really developing for it. Some of those games can be fixed by changing the plugin in Mupen64Plus FZ from the default Glide to Rice or another one from the list. It has always been like this with N64 where you gotta use different plugins to get different games to work.

And I'm also pretty sure that N64 emulation doesn't have 100% compatibility. I haven't tried Yoshi's story for over 10 years but on Project 64 on my PC I couldn't get it to work back in the day for example. That could still be the case.

But in general, you should be able to get all the big name Nintendo (Mario, Zelda, Smash Bros) and Rare games to work by messing with the different video plugins.