So... what if...
I enjoyed this film greatly as it really let you look into the strange ways people react to popular media. Heck. Whenever people ask me why my favorite word is Pareidolia, I can usually refer to this documentary.
http://en.wikipedia.org/wiki/Pareidolia
Though in the case of Kubrick I think one need to realize one possibility in order to not fall into one of these strange lines of thought oneself. And that is simply the possibility that maybe. Just maybe. He may have been an unprecedented perfectionist but he just might also have you know... goofed up a few times. Not realizing what some of it might be interpreted as. Even, like David Lynch has hinted about his own work, maybe he doesn't even himself know why the chair wasn't there. But he'd enjoy watching you try to work it into your reality because of how you look at his persona. A man who makes mistakes have things that don't make sense, but a man who is known as never making a mistake will make people look for improbable reasons for why the mistake is there. Or even inventing details that aren't there to begin with.
The Bible has the same strange situation. People would accept parts of it as mere poetic filling. But since it is supposedly inconcievable that anything there is wrong, we bend it and stretch it and re-interpret it mathematically, geographically, chemicly... etc in all these ways until we get to something that seems to make sense in the narrative and brings new meaning to the phrasings to the point that when the original texts talks about days it means suddenly ages. But it's bent out of shape enough so that it fits into the presumption that there are no such things as errors in the text.
So what I'm saying is simply that I love the works of Kubrick and I see the great workmanship that is rarely if ever topped in his work. But at the same time I need to realize that no matter how perfectionistic someone is in actions. The work they do don't necessarily have to be perfect and without authorial errors. Heck, people freak out so much because of the shadow of the helicopter that is only visible in OpenMatted releases while neglecting the fact that at one point in that same sequence the blades of the helicopter covers half of the frame. Hard to see in the flickering of 35mm projection, but clear as day in bluray HD. Put simply. He may have just goofed, but lets you analyze it because he wants to see what your mind comes up with.