Then, if they don't get it, have more obvious clues -- planted by the Dwarves who have figured it out and figure a mind flayer/PC fight is a win for them either way. If your players take out the mind flayers, they'll come back to face an ambush by an angry Dwarven army. Never pick a fight with Dwarves unless you're ready to fight every Dwarf in the world.
LOL; as they fled the Dwarven stronghold, Healer remarked "I hope we haven't sparked an international incedent." To which the mage replied, "Stupid greedy dwarves. How are they gonna find us? We'll be 1000 miles away by dawn!"