There's a reason for wandering monster tables...
If PCs rest in a dungeon or somewhere else they are trying to get into, the bad guys now have more time to prepare - bring in reinforcements, set up nasty traps, use more advanced tactics, etc.
If the PCs are "resting" outside the door of the big bad, just throw him at them right when they are settling down for the night - with some additional nastiness. Can't sleep in that full-plate armor, amirite? Oh... your spells didn't reset? oh noes!
Dungeons should be run as living things - if they aren't, the PCs have a tremendous advantage. Monsters and bad guys should aggressively attack their aggressors, and not hang back allowing them to rampage through the stronghold.