maybe it's more about how emily reacts in the heat of the moment when she discovers the truth. we don't know what they said to each other during the years they dated and raised MC.Then I am sorry about the people you did met, but yeah, I can see her being unable to see her own mistakes, just find it weird that the MC also believes is all okay i guest.
also, you can add to that that Andres left with MC and Emily probably still resents him for taking her son, her own flesh, with him.
we don't know how she views him now, after after a few days to cool down. she is too busy during spring break to even think about it anyway, with the murder stuff on top. it's only been a few weeks since the start of the story.
Mc taking the side of his mother is probably because of the fact that he hurt her a lot when he left. he only wanted to be far from Erynn, but he has now to take responsibility for what he did when he was a kid. There was a bit of a cheating story, but it seemed to be just paranoia from his step dad. Also, MC went to talk to his step dad and have an adult conversation, but again, they had a big fight in the heat of the moment, and MC didn't get to have a real talk with him. so Andres accused Emily to be a cheater, while he himself cheated and still cheats now just as he gets married, and ruined MC's relationship with his mother, and ruined MC's love life twice. There is plenty of material for MC's to take his mother's side.