I'm not talking about you or me or others who like to draw up maps and create dungeons. No, I'm talking about the mysterious men (and possibly women) who actually took to the task of digging the dungeons. They're all gone now. I mean, when was the last time your party went out to adventure into a dungeon that was being built? Never! Dungeons were built a long long time ago and filled with mysterious creatures eons ago. Whoever built them died off millennia ago because there are no new dungeons around. They're all worn out vintage things.
Along side their extinction these builders took many pieces of knowledge and power needed to build dungeons. I will enumerate a few of them here.
Gas - The arcane dungeon builder put methane detectors and eliminator in all dungeon settings. When was the last time your torch lit up a methane pocket in a dungeon?
Porous ground - Dungeon builders put water proof walls or built dungeons in places without ground water. Flooding in dungeons is rare, at least a lot more rare than in real mines. Mines have complex systems to eliminate ground water. Maybe this is done by some magic spell cast on the dungeon?
Radon gas - Yup, none of that either. Not that tracking radioactive materials with long term effects on the characters is particularly entertaining. Maybe that explains the giant rats? Which weren't so giant when they started living in the dungeon.
Collapse - earth quakes - support - Notice how a lot of dungeons don't have supporting structures. They seem to be unaffected by structural issues which plague mines. A Hold Ceiling spell maybe?
What dangers do you put in dungeons, aside from monsters, which add to the realism of traveling underground? Vapors from deep magma activity? Corrosive gases? Steam from a deep geyser?
Any adventure in which the party actually meets the dungeon builder?