Live by it, die by it...

[Cap'n Kobold]

Hmm. Just to be clear, I'm not talking about global rule changes.

I'm talking about breaking rules in localized situations or for specific NPCs.

It's not the same as fudging die rolls, but the principle is similar.

NPCs are not bound to have the same abilities as Player character Classes do.
This doesn't mean that they aren't generally bound by the same rules: unless they have a capability that says otherwise for example, they still have to make stealth checks to sneak up on a PC.

However it is generally perfectly fine to allow one-off rituals, spells or similar capabilities that don't appear in the PHB. If the party are going up against an evil necromancer, you don't need to sweat the details as to exactly how many undead she could be controlling for example.

 

[Jacob Lewis]

It is a fundemental flaw inherited when the collective decided that perception and insight granted characters psychic and omnipotent powers of observation. In essence, your in-game character gets a pass to peek behind the GM screen without even a die roll if the passive is high enough. If you watch any episode of Critical Role, you'll realize that "insight check him" is their favored way of engaging everyone they meet, including each other.

 

[Blue]

Hmm. Just to be clear, I'm not talking about global rule changes.

I'm talking about breaking rules in localized situations or for specific NPCs.

It's not the same as fudging die rolls, but the principle is similar.

Here's a guideline:
Taking players occasionally out of their comfort zone by taking away something they normally rely on is good. Look, you've been jailed and have no equipment. Or in your case "this specific NPC nemesis can't be spotted".

Regularly negating a character ability because you don't want to deal with it is a dirty move.

If what your planning is maybe one adventure every six months or a year, it falls into the first group. If it's coming up every few sessions it's the second.

 

[The Grassy Gnoll]

Re: secret doors - Investigation, not Perception.

Make things they have to ACTIVELY search for (and describe how) rather than Perception being the grand daddy.

Kind of:
Passive Perception = you know something is up as you walk in the room and so spot the Piercer on the ceiling
“I make a Perception check” = clenched fist signal, everyone stops, PC strains ears/eyes to see if they spot further movement, or if anything seems immediately out of place
Investigation = “I check out the bookcase, I want to pull out a few books and check the shelves to see if there’s a secret catch”

Different things.
Like Rorschach in Watchmen. He perceives nothing at first (maybe a general sense of ‘something’s not right’), but it’s his diligent Investigation is what helps him find the Comedian’s secret locker. Your high Perception PC could have that niggling feeling but still miss the secret door. How frustrating for them! And how cool for their team mate who does find something, having been given the heads up by Eagle Eye initially. Go team!

 

[iserith]

Or you might say, "Okay, Eagle-Eye, your passive Perception will apply to either searching for secret doors as you make your way through the dungeon or keeping watch for danger, when the outcome of those tasks is uncertain. Not both. Choose which is more important to you right now and you can always change later."

So Eagle-Eye is not going to notice that piercer and will be automatically surprised if he or she is searching for secret doors. Or he or she can potentially avoid surprise, but doesn't notice the secret door. That's a meaningful trade-off.

If Eagle-Eye does notice that secret door, he or she can then try to deduce how it works which may call for an Intelligence (Investigation) check.