Looking back at why, how, etc. a past decision was made is a waste of time and energy, IMHO.
Getting through Calc AB and BC with good grades in Junior and Senior years is sufficient and will put you on par with a majority of MIT applicants in terms of math (despite claims on CC that every MIT freshman has taken MVC, Linear, and DiffEq…).
One of my D’s best friends in HS was in her Senior year BC class and is now a Junior at MIT, doing quite well.
Do note, however, that this just means it’s not a big miss in one area of an application. Getting into MIT is very difficult and a vast majority of rejected applications also have been through Calc.