What a whimsical, funny game. I loved it. I only got to mystery 3. It seems when I play the clues I click (inkwell, pen etc) aren't populating in the clue book. I moved my mouse around the level and nothing else was highlighting so I had to give up after about a few minutes. But I loved what I played. Please keep building this!
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Thank you so much for playing and giving a review!
As for the bug(?) you mentioned, did you really click everything?
Some clues aren't 'noteworthy clues' so they don't show up in the clue book, but they're still relevant to the overall case (Phineas mentions this in the diner).
The noteworthy clues in the third mystery are the window, the Inkwell, the small note left of the pen and the bird cage.
The clues that won't show up in the book are the box of inkwells, the pen and the letter on the mayor's desk.
If these things didn't highlight and you couldn't click them then thats definitely a bug, however I could not replicate it unfortunately :(