"Can somebody explain me why ( aux.verb+not+subject+verb)
Aren't they going?
but (aux.verb+subject+not+verb)
Am I not going ?"
It's because of the word aren't which incorporates the contracted negative particle -n't [not].
The verb are and the particle n't cannot be separated in English; together they form a single word aren't. You cannot say:
Are they n't going?