Hm, that sounds like an rpg maker bug. That's known to happen if things move too fast, it skips some things and cause the game to glitch. I know rpgm also builds up issues if it's running for too long. I recommend saving often and restarting the game once in a while. I'll try to see if there's anything I can do to reduce this kind of annoyances.
Thanks for the report!
I wasn't aware of "running it for a long time might glitch the game up". need to save more often than I do, I guess. Also...you treated this report with more respect than I figured you would. Especially given that it's not likely something you can control. I appreciate that you took it seriously and offered a few simple solutions (save before big fight!)