Another question is was it Mary that knocked out Janine and the guard?
If so, Janine didn't seem to know it was her. No mention was made of it when she visited Sherlock / but as I keep saying, a lot of discrepancy has been hidden behind a few job dropping moments - its a device writers often use and one which would usually go unnoticed because not many other shows are still being analysed weeks later!

What also bothers me is the odd circumstance of Mary and CAM in CAM's bedroom.
His PA is in the office. It's not exactly night and why would he be there? In the bedroom there is almost nothing else where you would expect a vault.
Perhaps there was supposed to be a secret safe or strongroom? How would Mary know about that?
So he was alone in his bedroom while his PA and a body-guard or security man were in the office somewhere? Why would he be in his bedroom alone?
A lot of questions.
 

You'd expect him to have a bathroom in the office, too. But on the other hand we know that he is very sensitive where to release himself.

Mary was his dinner date..but she arrived differently and dressed differently to what he expected?

SolarSystem wrote:

Maybe he also changed (or wanted to change) his clothes, and I guess he would definitely do that in the bedroom upstairs.

Have you seen a cupboard in the bedroom? I am not sure that there is one.
I imagine that he had a walk-in cupboard or a room where he dresses and keeps his clothes. There is practically no furniture in his bedroom.

It's a bedroom??? How did I not notice that??

I have a theory that Mary first contacted CAM anonymously with an offer to sell him some blackmail material. CAM obtains his vast knowledge of dirty information that way, therefore he remained in the building and waited for his anonymous blackmail-source to contact him again that evening. Mary, who ensured CAM′s presence in the office that way, then entered the building secretly and she quickly taken out Janine and the bodyguard before they could see her. (Janine especially would be dangerous in recognising her).
 
I think Mary was not trying to kill CAM when Sherlock walked on her – she was rather threating him and scaring the hell out of him in that scene. She probably wanted to obtain something from him (that A.G.RA disc, maybe?) and it would be most inconvenient for her if he was dead.
 
The thing was different with Sherlock, through. Sherlock could oust her to John as an assassin. She therefore shot him while leaving CAM alive.
 

I based my theory on the fact that it actually happened that way in the original story.
 
If Mary contacted CAM as an anonymous source of blackmail-information and he was awaiting her in his office, it is even possible that he personally let her in (people were always wondering how she entered that place without Janine allowing her in and this is a workable solution to that problem).
 
Mary knew she is CAM′s target from the moment John was stuck into the bonfire. She had plenty of time for preparation for her attack on CAM and her frienship with Janine allowed her to obtain information on how CAM′s office is managed.
 
What we also know: Mary took CAM hostage in his office and she then forced him to go into his personal quarters. When Sherlock was investigating CAM′s office he noticed CAM′s chair being still warm and Mary′s perfume still lingering in the air. But why would Mary be taking CAM on a scenic ride through his office and his quarters if she just wanted to kill him? She is a cold-blooded expert in murder, obviously, so it would be a piece of cake for her to shoot him dead immediately after entering his office.
 
The answer is – she didn′t want to kill CAM yet. She wanted to obtain something from him. Probably her files (if he remembered them while listing through the memories of his mind palace, then he definitely read them in physical form in the past). But because that fiasco with Sherlock happened she was unable to force CAM to give them up. And it would be most unpleasant for her if she shot CAM dead and the police would then enter Appledore while investigating his murder, finding her files in his vaults. (No one knows to the very last moment that CAM′s vaults exist only in his head).
 

nakahara wrote:

I have a theory that Mary first contacted CAM anonymously with an offer to sell him some blackmail material. CAM obtains his vast knowledge of dirty information that way, therefore he remained in the building and waited for his anonymous blackmail-source to contact him again that evening. Mary, who ensured CAM′s presence in the office that way, then entered the building secretly and she quickly taken out Janine and the bodyguard before they could see her. (Janine especially would be dangerous in recognising her).
 
I think Mary was not trying to kill CAM when Sherlock walked on her – she was rather threating him and scaring the hell out of him in that scene. She probably wanted to obtain something from him (that A.G.RA disc, maybe?) and it would be most inconvenient for her if he was dead.
 
The thing was different with Sherlock, through. Sherlock could oust her to John as an assassin. She therefore shot him while leaving CAM alive.
 

 
I like this theory. And it still enables Mary to enter bamfly through the window rather than going through the lobby. She wouldn't want anyone to know she was there. Whilst I agree with you that she almost certainly set it up with CAM to expect a visitor from an anonymous source who wanted to sell him blackmail material, thereby ensuring he stay in the building, I do think she was on her way there to kill him.

If he was already expecting her and she had no intention to kill him, then she could have just entered normally through the lobby. The only reason she didn't was because she knew she was about to commit a major crime and would have to make a swift exit and not be seen by anyone.

Plus, later on she states that people with Magnussen deserve to be killed.

I know she could have killed him immediately as soon as she arrived, but she probably intended to get the files she needed, then shoot him.