Ms. Chalice's mole swaps from right to left all the time, like when she swaps from her ghost form. When she is in her ghost form, it is on her right, but when she swaps places with Cuphead or Mugman, it swaps to her left.
When you start the Devil's phase two and the song changes, a sound effect plays in the song and in-game at the same time. You can hear it yourself if you pause the game when the sound effect plays and still hear it in the song, also delaying the sound effect.
If you get the bad ending after unlocking Ms. Chalice, Cuphead, Mugman and Ms. Chalice are seen next to each other. This should be impossible, as when Cuphead or Mugman eats the astral cookie, they swap places with Ms. Chalice, changing them into the ghost instead.