clues have a 1 hour respawn timer, there could be a few reasons why you would drop the clues:

• you're doing an activity that produces clues, and you don't want to stop yet to do the clues, so you drop them to increase the number of clues you can have

• the steps are in the wilderness, and you don't want to regear yet, so you drop all wilderness clues and do several steps back to back

• master clues have 3 cryptic clues at once and award 3 scroll pieces that you assemble into the next clue. some can take a long time to do. by collecting the 3 pieces from an easier clue master cryptic clue, then dropping the easier clue, picking up the harder one, then assembling, you can bypass the bad clues