Not sure what's going on. I would need the MIDI file to test it out. What version of PICO-8 are you running.
If you can hear it through the PICO 8 player embedded in the web page, then the music data generated correctly and should be a simple copy and paste into the music tab in PICO-8.
If you post the MIDI file to the PICO-8 discord server, I could take a look at it. My screen name is bikibird.