ExploderWizard
Hero
Knowing one thing is undesirable does not mean you have a specific outcome in mind. Imagine a large sports field with a fenced off hole. The players can go anywhere on the field except into the hole. Why? Because falling in the hole is a problem for play.
If the hole is a problem for play, why did you play in a field with a hole in it?
If an adventure is designed so that it works out unless the players do one specific thing to muck it up, then you can count on the players doing that specific thing.
EVERY. SINGLE. TIME.
No one knows why, or how this happens exactly, but despite the astronomical odds it just does. This is assuming of course that the players have no idea that the thing that they just did was "off limits".
If they DO know of any such limitations then just not might likely happen, they will STAMPEDE towards it.

Play a little mini game when designing adventures. If you can easily identify pitfalls such that they resemble fenced in holes on a field, address them directly before players can discover them.
Identify each of these holes and run a session of PHA ( plot holes anonymous) for them. Let each of them share with the group.
" Hello everyone. I'm Bob, the super duper hidden secret door on level 6b, and I'm a plot hole"
Hi Bob
" So I'm really important and behind me is the only clue to finding the smugglers. If the players don't find me with my ridiculously high DC then they will have no idea where to go next. "
Why are you the only clue Bob
" I dunno. The DM really wants me to be a challenge but he also wants the campaign to keep moving forward. I suppose the only thing to do is make sure I get found SOMEHOW."
There is a better way we can do this Bob. Why don't we move the vital clue needed to continue to a spot that is hard to miss. Behind you, we will conceal maps, charts, and other writings that will offer valuable insight into the smugglers immediate plans. Without this cache, the players can continue but it will be more difficult without finding you.
" Wow! Thanks. Now I'm still really important and not not a plot hole!"
If you can identify them well enough to build a fence then you can fix them.
