Overview:
When running the territory rules for a particular node in Salesforce, accounts are not getting assigned even though they match the Territory Rule criteria.
Root Cause:
The lower level Territory is inheriting the Territory Rules of a higher level Territory. Identify the Territory by checking the Inherited Account Assignment Rules section for the Territory that the rule is run on. This information is found under Setup --> Manage Territories Territory Hierarchy --> [Territory]
Solution:
Disable (uncheck) the Apply to child territories checkbox on the rule for the higher level Territory. This is also found under Setup --> Manage Territories Territory Hierarchy --> [Territory].

Related Documentation:
Salesforce Help Documentation: Territory Management
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