The one game I am aware of and keep checking is "Wonder Project J2 - Koruro no Mori no Jozet".
Broken in both Ares and the miSTer core. AIUI nobody knows why it does not work yet, which shows gaps in the understanding of the machine. Otherwise not an issue for me, as I can run it on the actual hardware, which I own.
Note that, in no small way, I do appreciate the efforts. The state of the art of N64 emulation is much better now than just a few years ago. But it sure is not there yet.