Thank you for your reply! We are taking a look into the issue where enemies are not registering damage. This is a complicated bug since we can't reproduce it. Definitely hard to do.
We never opened 2 games at once, so that might have created a huge conflict with save files, since (for now) there's only 1 save slot created by the game. I believe that it could have created a conflict between the 2 and the save file was considered inexistent because one of the games did not have one.
For the edit portion:
We will check a way to make the noise appear when spawning on top of the player. Thanks for the input.
The ghost spawning is a problem, so thanks for finding that out. We will check a way to make sure it doesn't happen.
About the indication for changing time, this was an oversight on us. Thank you for noticing. We are actually building a mini-tutorial-ish similar to the other indications we have in-game. It will be an update very very soon!
We believe the enemy issue then is happening with the transition between time, since some situations in-game pause the flow of time for a bit (like cutscenes and boss fights). Maybe if one of these events happen during transition, we think it's breaking the system, so we need to look into it.
The trumpet fish bug seems to be related to the pause, so we are working on a fix for it. Sorry about this situation.