It's more like, the Mom had time for the Sister, but never had time for MC, because she had a false sense that her Son could manage stuff by himself without her help while the Sister couldn't.Because of her work, the mom never made time for her kids or care to listen to them, especially Yukito. It was to the point his sister Yuri has to take care of him. She neglected her kids.
The mom first realized her mistakes during observation class in elementary school where Yukito didn't care to look at her. Add the incident where Yuri almost killed him and he disappeared for 6 days. The aunt stepped up and yelled to her sister how a bad mother she was and took in Yukito for some times.
So now, to make amends she tries to overcompensating by giving him more love than back then.
If I remember correctly, there is also an incident which occured in elementary school where it lead to Yukito being bullied. The teacher thought he really was the culprit at that time and didn't believed him, even his mother didn't. Also, virgin killer neighbor was implied in this mess because she was a teacher in training and worked with Yukito's teacher.
On the otherhand, MC had been a mama's boy since childhood, which is why he tried to avoid causing her problem as much as he could, even doing all the work possible by himself. MC was such a mama's boy that it was hard for him to look at her when she dressed up nicely (this is the reason why he didn't turn around during the parents meeting, which his mother mistook for something else).
There was also the issue that, though the Mom believed that MC could manage to do stuff by himself, she in a way never really trusted him, as if any issue occurred, she would always react as if it was MC's fault.
The main change point for MC was the incident with his sister.