If he's normally a good, well-behaved child, and he's scared or "doesn't like" the bus aide, I'd want to investigate the bus aide business first. If that's really odd behaviour for your son, there's a reason.
School is almost out, so perhaps there is an alternative quick fix until it's over.
As for what to say to the teacher, your son is the one who needs to do the talking, not you. And, he needs to make amends to the teacher, something that STICKS it in his mind, something that will impress upon him that there are consequences.
And, yes, I can't fathom in this day & age that a school would allow a child to depart campus without a note or parent/guardian, so you should address them on that.
What a mess!!! But, look for the root and nip it.