With a hack as complicated as Lunacy Mode, it should come as no surprise that there were some glitches that were harder to detect than others. Players on the Lunarian Shuffle's Discord server reported some errors they encountered. Re-download TLS to update to v1.122 and get the fixes to these errors.
In particular, the Zeromus fight had three separate problems afflicting it, which would either short you a character, or duplicate a character, or the game rarely would outright crash as it attempted to begin the final battle. The crash was as much Squaresoft's fault as it was my own - apparently, the interrupt that draws the next screen each time the current frame ends will completely fail if their own RNG was in the middle of executing.