I was on a tour today, so I apologize for only reacting now.
Let me fix that real quick.
Someone entered Stanleys room through the window, killed Stanley, then Natalie unlocked the door, entered the room, Stanley's killer exited the room together with Natalie thorugh the door.
Natalie didn't let any killers in or out of Stanley's room before you found him.Simon's murderer had entered his office through the window, killed Simon, then closed the window/removed any clues that would lead someone to suspect that the killer entered through that passageway. Another person then unlocked Simon's office from the outside with a relevant key, and then, the killer exited the room, and the door was then locked afterwards from the outside by the other person.
It was clever how you avoided all previous red truths up until the last 2 words. This previous truth however modifies your truth a bit:
Between Simon's death and Alfred unlocking the office door, only Simon, a witch or Simon's killer could lock the door from the outside with a relevant key.
The modified red truth would require Simon's killer to lock the door, but that is prevented by this truth:
If Simon was killed, his killer didn't receive any new keys between first exiting Simon's office after his murder and you finding Simon's body.
You seem to be in a stalemate with Simon's mystery. I don't want to unnecessary elongate the real challenge, so I might just exclude a major option right away.
Simon's office doesn't have any windows.It will be challenging enough without this extra distraction.
To avoid further unnecessary distractions, let me get this out of the way too:
Only Alfred's "dark room" mystery involved secret passages.