If the system doesn't (and any game with prompts for doing things can get confused by this) then it can be a point of frustration and failure. (not constantly, but often enough to be a constant reminder and source of caution)
Say you are escaping guards and want to jump on boxes, but you are approaching diagonally to the boxes edge and the game doesn't recognise the box and doesn't give you the prompt for jumping. Variations of this happen often. And instead of the player having to get used to how high and how far you have to jump to reach something the player has to get used to the logic of the prompts. (which is harder since prompts depend on a more intricate logic than jumping)
Any game which has had a prompting system for doing things like this has frustrated me at least in one point due to not giving me an option when I can clearly see I should be able to do something or getting me killed because the "knock out" prompt didn't appear while I was clearly behind a guard. Whatever the case removing the player's ability to do these things when and how they wish is just restrictive gameplay.
Lets say melee is a prompt, if you are not correctly facing the enemy you can't swing or do nothing, so it's not as fluid since sometimes you end up just standing there stupidly doing nothing at all while the enemy notices you and shoots you in the face. (I believe I've experienced this most with Hitman, but also with the Splinter cell games)
Sure it makes it easier for the devs to plan player paths and approach options, but it also restricts and limits the player imho.
I'm sure there will be a situation where you are sure you should be able to jump on something or reach something and will circle around the object for ages and then leave because the level designer had built something like it should be reachable, but has decided that it shouldn't be reached or forgot about adding a prompt option.