So, about the first puzzle... Me testing it is a bit hard, because I already know the solution. What I did to test was just randomly pull the levers, then at the end set the good combination, and the door opened, no problem.
I really want further details from you and do not want to guess, but I explain what I think might cause the confusion. In this puzzle, you are not actually pulling levers, are you are entering a code. By that I mean that activating certain levers is just as important as not activating others. But deciding which lever position counts as active and as inactive is not expalined to the player (this is definitely my mistake). What I should have done is adding noises or lights or something, to indicate if the player is on track towards the solution, and to make sure they understand how the levers work and which position counts as active.
Did I understand your issue correctly?