Baby Mario doesn't like Baby Bowser. He used him to lend him up the shelf to reach the dimensional remote and not fulfill Baby Bowser's wish for him, which was asking Bowser's mom for cookies because he was really hungry.
In Mario and Luigi's Stupid and Dumb Adventures, Baby Mario is shown to actually be Mario as his past self, along with his brother Baby Luigi, who's Luigi's past self.
It is unknown why Baby Mario attended to Bowser Junior's class.
When Baby Mario neglected Baby Bowser in MALSADA Season 3 Episode 3, it could also explain why Bowser doesn't like Mario from the start.