Looks like a bad sdcard or unstable overclock. What 'single commands' mean - running a game or actually starting a program ?

Please add more details about your setup, as asked in https://retropie.org.uk/forum/topic/3/read-this-first.

If I do sudo apt-get update and then sudo apt-get upgrade it also locks up doing the upgrade. But I was able to both of these in Raspbian and Raspbian lite.

Okay, I'm not sure what happened, but suddenly Genesis games work. I'm not sure if it was bad roms like @mitu said or if it was bad naming conventions on my end (changed both at the same time), but seems to function now either way.

Thanks again everyone for the help!

Yeah I noticed those. I just left them at the default settings. I will try to disable them.