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"