The friction between Maggie & Michonne is also in the comic. I don't know if they are going the same way on the show or not but what happened is...

 

So Maggie sort of turned into Morgan and "Lost Herself" as well. Now she's got to embark on a sort of vision quest with Georgie and Co. to find her marbles again!!

 

If you remember in Rick's last episode, the saviours attack the camp. It was mentioned in Ep6 when Carol and Henry got hijacked that Carol had actually let some surrender and run.

My theory:
Maybe, only that small group stayed out of the way but the rest of the sanctuary retaliated at their friends being killed (the ones Rick saw at the camp), sparking another small 'war' between them and the other communities. Maggie was against the saviours anyway - wanted them to do all/most labour at the bridge without extra resources/food. She probably wanted an end to it all and ordered an attack. Michonne, grieving over Rick and wanting to respect his wishes of communities uniting not dividing, stayed out of it. But somehow her and Daryl got caught up (maybe captured). They get their scars, and is finally rescued but the sanctuary eventually falls. Michonne blames Maggie for going against Rick's wishes (afterall she spared Negans life so she thought she was on board). Both their hearts and egos are bruised. Maggie feels remorse and guilt and they both decide it's best they no longer communicate - the hurt is too much for both of them. Daryl commits to finding Rick (walker or human) and to being the best person he can be without dragging anyone into harm (like he did with Rick, resulting in his 'death'), by going out on his own but helping each community when he can. Maggie finally reads through Georgie's letters and finds it would be a much better place to raise Hershel so she makes the decision to leave, giving promise she will return when the time is right and old wounds have healed. She leaves Jesus in charge, against his protest. Tara sees Jesus is struggling with the new leader role and becomes his right hand woman.

For whatever reason Maggie left and her and Michonne wasnt talking, it was also 'promised' that Michonne wouldn't be told. Is this because Maggie didn't want Michonne to go to the hilltop ever again? OR because it would cause too much pain for her knowing that Maggies was no longer there? Michonne looked shocked - but also hurt that she hadn't been informed sooner that Maggie wasn't there. Maybe she is now feeling guilt and remorse for things in the past.