We have the same issue which is leading us to customize the system to avoid this validation error. The Validation should be on the unique combination of CNPJ and IE.

Also, it would be good if the validation were to be extended to the addresses as well and the fiscal documents populated from the applicable addresses rather than the primary master record. If a legal entity has more than one IE per CNPJ, adding the additional unique combination as an address should allow for the use of the CNPJ and IE population from the Site address for fiscal documents related to a sale. Likewise, when purchasing from a vendor with more than one IE per CNPJ, being able to select a purchase from location on the PO and invoice would help like is possible like a Remit to Address on an invoice journal should allow for the correct population of purchase fiscal documents instead of duplicating vendors in order to correctly populate the CNPJ and IE.