Just going to leave this here...
I changed general video settings in the mupen64plus.cfg to (this didn't fix the issue for me)
Width of output window or fullscreen width
ScreenWidth = 800
Height of output window or fullscreen height
ScreenHeight = 600
Next, I changed general video settings in the mupen64plus.cfg to (this didn't fix the issue for me)
Use fullscreen mode if True, or windowed mode if False
Fullscreen = True
Neither of these worked for me. I finally put a fresh image on my EMMC and that fixed the issue.