If your players misinterpret clues to a mystery do you do anything to correct them? Do you let them run with it and hope that they'll eventually figure it out? Do you tell them out of character what happened? Do you reiterate what they've already ignored? Do you laugh maniacally on this inside?
In my game a cultist was strangled by a skeleton when the cultist opened the sarcophagus. I clearly described that the strangulation marks were from skeletal hands, I said something along the lines of "you can tell he was killed by a skeleton based on the strangulation marks coming for a skeletal hand." But the player decided that didn't make sense because "the skeleton would've attacked with his sword" even after I reiterated it was a skeletal hand that strangled the cultist. Now the group is trying to figure out which hired henchman of the cult is a traitor. (Ultimately it shouldn't take anything in the wrong direction, but they're looking for something that doesn't exist due to an assumption made based on game mechanics rather than story.)