@Guillaume Hmm, yeah I'm not sure what's going on. I finished case 3 on Normal mode (or whatever's the highest you can pick at the start) and got the S rank on the final puzzle, which is a lot later than I did in the first two cases. I didn't use any hints, and I stopped doing the "wrong" answers, so I'm not sure how this scoring system works.
I hope I don't miss out on any bonus puzzles. To be honest, I'm not very invested in the story or characters, so I really don't mind when a conversation is suddenly interrupted by a puzzle, haha.