I just finished playing through this on emulator (Gens+), and noticed that there's some glitchy notes in the final boss music (Estrayk - No Mercy).
I might give it another try on my Everdrive at some point to see if it happens on actual hardware as well, but I figured I'd mention.
It's honestly the only flaw I've found in an otherwise amazing port, I had a blast playing through this again. =)