Of course, some cats could - at least theoretically - describe a hyperspatial catenary that would mean they could circumnavigate the 3-d physical constraints of 'doors' or 'windows' (if they circumnavigate the constraints of Windows, then thy're either using X11R6 or Mac OS X), but given they do not have Narcissistic attributes, they are likely to hide their stupendous metabilities under a bushel, so to speak. This means they might do their business in a less than optimal environment, if they think mere humans are watching for demonstrations of higher mind powers as manifested by the Real Elite of the Universe.
Generally, Cats would probably prefer to 'go outside' when they can, but unless they have been trained, it is not reasonable to expect them to be able to signal when they need to go outside.
I am rather concerned about the whole idea of 'indoor Cats'. They're not designed to be 'indoors' allthe time and to deny their essential nature is not a good thing, for them or for the people who try to tailor them to function in this manner.
All I can suggest is that if you must keep Cats indoors all the time, then you do not 'punish' them for occasional lapses in toilet ettiquette, rather spend the time necessary to train them to live within such a strictured and controlling environment.
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"The power of accurate observation is called cynicism by those who have not got it." - George Bernard Shaw (Taken from someone on comp.programming)