I think your examples fall into quite different categories.
Things like extent/extant then/than dependent/dependant (in British English) could just be a typo, one real word typed for another.
Many other examples seem to be related to the fact that the letter in question is pronounced as an unstressed schwa. If there was a word "seperate" it would be pronounced the same way we pronounce "separate". If there was a were "existance" it would be pronounced the same way we pronounce "existence". So if you've heard the word a lot but not seen it written, those mistakes are quite understandable.
Analogy plays a big role in this sort of thing, e.g. compatability for compatibility by analogy with capability, etc.
