The Admin User runs a Mass Assignment from the Territory Utilities tab on one of the top level territory nodes:
The Mass Assignment processes all Zip-to-terr and Brick-to-terr records regardless of Territory. The Org has multiple top-level Territory nodes.
This is expected behavior. When multiple top-level Territory nodes exist in the Org and the Territory Mass Assignment is launched on one of these top level nodes, the assignment process includes every Territory in the alignment.
Create a single, top-level Territory above the existing ones. If a single top-level Territory exists, the Mass Assignment work as expected on the selected Territory.
CRM Help Documentation: Territory Management
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