SQL Change Automation adding permission assignments in the view script and creating schema for role

The project includes a filter that excludes users, roles and security policies. But the baseline script is including object permission assignments to users and roles. I edited the baseline (note that it was not yet checked into and not yet verified in the proj) . After removing the assignments from the baseline script then after the refresh some view scripts include permission assignments and one of the roles (excluded by default - since all roles are excluded) is being scripted as a schema.
What can I do to halt this behavior of assignments in the project, since all roles, users and security policies are removed? 
This is related to another question I posted today, also (10/30/19).