Corrected entry: When the colonists go into the cave to escape from the Crystalline Entity, you can see perfectly formed steps going down into the cave. The colonists were the first people there. Why would there already be perfectly formed steps in a cave?
Corrected entry: When Dr. Marr arrives on the Enterprise, she states that she's excited because there have never been survivors from an attack from the Crystalline Entity. They also state that the Entity consumes all organic matter (including bacteria) and leaves none behind. Later, when Dr. Marr and Data are inspecting the cave the colonists took refuge in, she states that on two other planets, victims took refuge in caves and still perished. Now if the Entity consumes all organic matter (including bacteria) and there were no survivors, how would they know where the colonists took refuge, or even if they took refuge there at all? If all organic matter is gone, then there would be no trace of the colonists remaining.
Correction: Synthetic clothes, equipment, luggage, any non-organic items the people had on them would be piled up in the caves. Once you know you're dealing with something that consumes all organic material, it wouldn't be hard to figure out what happened when you find a pile of polyester shirts and piles of keys and such lying in a cave.
Correction: There is nothing in the episode stating that the caverns had never been used before.