All of what you describe are also things that I've experienced and that needs to be addressed. Every scene change sequence needs to check what the current bgm audio stream is playing to see whether it needs to be changed to what's supposed to be played at that area in that situation – and if the correct bgm is already playing, it should not be restarted. That's an easy fix, assuming that there is a function call that can check what's currently playing.
Another thing that really messes things up is that many of the newer romance events that are supposed to transition from night to day don't actually restore your energy and some don't actually even transition to a new day, even though the day counter for the "Orderboard" certainly seems to change – but not the normal day counter! I'm not entirely sure of exactly what's going on there with the day counters, but I'm fairly sure I lost the chance to turn in a couple of contracts because of the transition issue. All of the events that are supposed to transition to the next day need to be cleaned up so that everything adjusts properly.
All in all, there are a lot of issues like these that are simple to fix and honestly simple to avoid in the first place, if you just pay attention to what you're doing and don't rush to complete things. It's always better to take some extra time to finish something up real good if it needs to be. That's especially true for indie software development. Nobody's really dependent on it to be completed at a certain date to save their livelihood. So whatever you do Team Bieno, DON'T RUSH THINGS! Do it right or don't do it at all.