Impregnable comes to English from the Old French imprenable and means unable to be captured or broken into; impregnatable comes from the Late Latin impraegnatus and means to make (a female) pregnant or to be able to be permeated.
The two words are etymologically related only by mistake. The added -g- in impregnable, and the subsequent confusion between the two words, can be blamed on unknown Renaissance-era philologists, who likely mistook the word as a relative of pregnant.