How I Met Your Mother Theory:
After Ted meets the love of his life he gets married, the children young have very little memory of their mother because she died in a car accident very similar to the one Ted was involved In at the end of season 3. Years later he re-marries… Robin! Because her and Barney had a nasty breakup. So those time when the kids ask when mom gets home it’s referring to Robin. Not their birth mother.