Clues are different than secrets. Clues are used to solve Mysteries, which in turn unlock buildings. When you find a clue, the game will identify it as such and save a snapshot of it under the "Mysteries" tab in the menu. Clues may contain passcodes or other information that must be used later. You do not always have to find all the clues to solve a Mystery. Most Mysteries have a single Puzzle Object, which is the clue that you actually have to interact with to solve the Mystery. Returning to find clues after solving the Mystery will still trigger a notification and add them to your clue board. If you find a clue then exit the level, the clue will still be added to the clue board. However, you will not get a checkmark on a level, even if all of its secrets and clues are found, until you actually finish the level by eating insects. Most clues are found within the building which Mystery they help to solve. However if you find a clue and the "clues found" total on your current Mystery does not increase, it indicates that the clue is used for a Mystery in a different building.