Have you checked the Aggregate Missing Values Option at Database level? If it is not checked, then it will not aggregate the #Missing data at level0 to the parents.
You have to restart the database to take the property in to effect
You can even set this at Calculation script level
Please take a look at the article of the blog. It's not my blog but the situation is similar.
-Sandeep Reddy Enti
If you enable aggregation of #MI values at server level, it will be applicable across all apps/db.
Good approach would be to use SET AGGMISSG ON in the business rule
Set AGGMISSG ON efore you aggregate the dimensions and then set it OFF after aggregation. This will enable you to control aggregation of #MI