Meld into stone was a nice idea, and I didn't see it coming.
BUT a tracker of the clear expertise of Oona (who can distinguish between Durkon's and Minrah's feet) would immediately notice that the tracks end up suddenly in nothing. "They apprently disapperead in this spot".
Not sure Team Evil knows about meld into stone (they could think the dwarfs used Plane Shift, for example), but surely enough they wouldn't need to enter the dungeon.

About the marks on the door, MitD asked explicitly at least once to paint the doors. If this is what happens usually, they will have no problem to track the problem to it.