Could Maggie have left where wver she was back home, most likely the Commonwealth or a rebuilt Alexandria before Rick got back? Is this at all possible? She would have had to have been at the Bricks a lot longer than portrayed on Dead City. The timelines in TWD have always been open to interpretation.

While the first season finale of The Ones Who Live shows Rick and Michonne being airlifted to a safe place to reunite with their children, the name of the location is not given. However, in the fourth episode of the miniseries, the couple agreed to go back to Alexandria to take care of Judith and RJ together.

But this is ambiguous as the definitive location of where they land immediately on return is never divulged.