It's a great idea that you intend to check every area. When you fight Rabbid Bandits (no. 256) or Bright Riders (no. 288) in the Rabbit Tunnels, the bestiary loading issue occurs, too, even if you've encountered these monsters elsewhere before, because the bestiary entries are "overwritten" with a different battleback, which makes me think your guess is correct. Man, I miss the days when checking the bestiaries in RPG Maker MV JRPGs simply made the game crash. ;)