Just a couple plot questions... [spoilers]

[Razalhague]

Ack. I've explained that one a whole lot of times. That's not neccessarily a plot hole, why would it be? It is fully possible that Anabel just standing somewhere in the middle of the room when Philip charged in, started running around like crazy, and she was like "?". He turns around, starts running towards the corner of the room and she goes to stop him - and passes just below the weight thing just as he drops it.
I can't remember how it works in the game, but didn't that weight drop pretty fast? If so it's very possible she just passed under it, didn't even think of it's existence and wham - was hit on the head.

You have to get the weight up first yourself. One would think she'd pay attention to something like that.

You even disproove yourself a number of times there, don't you?
Several problems with that theory:
1. Clarence does want to kill Philip, either so that he can get out of his "prison" of a body or so that he can start freely manipulating Philip's body like his own.
2. Amabels voice never sounds infected, nor is she infected when you see her dead body.

I've got to rush out into the real world now anyhow. End of post.

Point number one, I admit it's a bit ambiguous whether he wants Philip dead or not, but I don't think so (not until Philip's ready to get rid of him). I trust his actions (warning Philip of danger) more than what he merely says.

As for point two, you didn't pay much attention to my post, did you? I already explained why neither of those is a problem. The doctor who tries to saw off his hand sounds completely normal (aside from the random facts he occasionally spouts) only a couple of seconds before he busts out of the door as a mindless infected. And her "uninfected" dead body is just Clarence playing tricks on you.