Specifically, a design flaw in how warfare was modeled, intended to allow Crusader armies to reach the Levant without fighting across all of Christiandom, also allowed the Muslim armies to reach Europe without fighting across all of Christiandom, and the AI didn't always respond to this by trying to kick them out. In practice, this led to little isolated Muslim enclaves in places like Bohemia, France, and England, surrounded by vast Christian forces that really didn't care at all that Prague, Paris, Rome, and London were in the hands of the infidel. Of course, CK had a horribly convoluted development history because of how Paradox got the project dumped on them in the first place, but still, oops.