All games can be filtered without any major issues other than the exit bug I mentioned.
I played SM64 DS, Metroid Prime hunters and the two Zeldas with Render Scale =2 and I haven't got any problems yet.
I also played Chrono Trigger but that one doesn't have 3D models haha
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Maybe, but I heard
@dimok also stumbled upon the same bug with Mario kart 8 with updates I think.
So I don't know what it might be, but that's most likely it, and if that's it, then it only solidifies how lazy they were when making the emulators.