Gamify this stuff. Instead of a single silent alarm causing the players to get ambushed, have a threat level that you're tracking that requires multiple triggers to end up in the worst case scenario. Give players in-game feedback that this is happening (they notice there's a higher frequency of patrols, overhear guards getting new orders, etc). Give players mechanisms to reduce the threat level (waiting until things cool down, hacking security systems, stealth takedown of guards, etc).

As much as it is tempting to do pure simulation in a realistic way, it doesn't always make for a fun game. Fun almost always comes from interesting and meaningful decisions for the players. Having invisible triggers going off behind the scenes that the players will never know about is only interesting for the GM.

Just off the top of my head, you could give them a flaw that, while it doesn't make them any less cunning, it does let the players see what's happening.

Method 1: Gloating. What is the point in being a genius if nobody ever notices? When the villain has the party on the ropes, have them point out moments of the plan that the party could have noticed but didn't. Maybe they wait to give the shopkeep the bounty until the party can see it happen, just so they know.

Method 2: Worse minions. The plan is amazing, but the people carrying it out aren't quite as discrete as the villain. Maybe the security make a little noise as they stalk the party, and there are moments where the players could spot them.

Either way, the players will know something is up, and might have an opportunity to use this new information to turn the tables on the villain ("might" and "opportunity" being the key words there).

One approach would be to tell them.

Not everything that the GM says to the player necessarily needs to be character information.

Of course, you don't want to ruin their suspense by telling them too early or too directly, but something along the lines of "as you hear the sound of many footsteps closing in, you remember that you thought you heard a "click-thunk" back in the mansion, but brushed it off as your nerves back then ... maybe you did trigger that silent alarm after all."

Blades in the dark, the Forged in the dark games, or White lies have a way to do this.

First, the character do the plan, not the players. It means that the planning phase is just an ellipse and players have a limited flashback possibilities (ah yes, but in fact it was a possibility so my character knows that .. or has the need tool to ...) and they use clocks (4 to 8 pieces pies that are filled step by step, ok so one more tick on the "general red alert" clock, only to remaining).

If you want an actual play of blades in the dark: Oxventure https://m.youtube.com/playlist?list=PL8DF056nV-PUFQbq2TlAzT4BP7pjRhwml

Are you a shadow run gm?

Some thoughts, in a chaotic order

In general I try to GM in a philosophy like *NPC are person whose action reflects their "supposed skill level", who don't want to die and act rationally". It makes the whole story more realistic, limits the combat (Because NPC don't want to die). However, the how optimal they act is one of the tools I used to balance the game. Stuff like a sub-optimal combat tactic (not finish the already injured PC) or the good old waiting for the orders

A big issue are the "secret NPC reaction". An option I use a lot (in game with failure margin) is to stack-up the failure margin of the stealth roll, like PC know that they're doing noise,but don't necessarily know how much noise would wake-up the guard, trigger a silent alarm or have the special forces storming the complex (I know Blade in the dark has the clock concept which are similar). A more radical variant would be the PTBA-like consequences like you "do the action but someone acts in the background against you" which help the PC feel the "risk level getting higher" without the binary everything is fine --> A sniper just killed your character sorry. I've seen some game having reputation mechanic which is a way to put a number on how much a faction hate/like you. Which again can be used to increase the paranoia level.

Finally, if the PC understood the story differently than what I was planning, and that it make sense with what happened. I would change the plot to adapt to the PC understanding. Think about improv theatre were you're expected to say yes. If I wasn't clear with setting my scenario and the player go in another direction let's accept it rather than force the party back on the rails. there is obvious limits, like NPC aren't "that stupid"

I don't think the problem statement has been clearly articulated.

Have players complained about events which they felt were unfair and unjustified? Are you concerned that they're missing out on the background that would improve their enjoyment?