Some more so-called wisdom earned while doing my long-last first megadungeon.
Revise, revise, revise. Sometimes while I'm stocking, I realize what I put down can't be there. The dragon can't get out, the orcs can't live there because they can't get past the vampire, etc. Or it's architectural - the only thing that makes sense in the little corner is a door that's not on the map.
So I revise - I add tunnels, I block off rooms (would you leave a nest of infectious zombies a door to your lair, or brick it up?), and I fill in extra places.
Nothing is so perfect that you might not create choke points you didn't intend, or open up ways up and down or side to side that you wouldn't have.
And again, sometimes it's the luck of the stocking roll.
Never be afraid to fix something after you find out that what's in the room can't be there without fixing it.
So you're thinking you could just come up with a good reason why the dragon is there anyway, how the orcs got stuck, why the door isn't bricked up yet. And that's fine - but which takes longer?
Corollary: It's a matter time-to-benefit ratio. If you can take five minutes and come up with a good reason, great, do that. If it's going to take longer, it'll take less time to make a bigger door or draw an extra corridor or note the door is bricked up. Choose the more interesting option when possible, but don't sit and agonize over something you can fix with a couple of pencil strokes on the map.
If you think of a better idea later, use it someplace else and put the "mega" in "megadungeon."