This is not totally clear and has tripped me up severla times. The Order by statement in the Models advanced tab does not accept Field Alias values. You have to put the full function + field value there. Here is an example:
I have a model aggregating dates by Year and Month.
Then the Order By Statement looks like this: CALENDAR_YEAR(Date__c) DESC, CALENDAR_MONTH(Date__c) DESC, DAY_IN_MONTH(Date__c) DESC
Pro Tip. In order to have a Year, Month and Day grouping on the same field - you need to jump over to the XML and add the second and third grouping row.
