Hi thonas,
If the importer of the goods is VAT registered in the UK then the shipping agent should have been provided with the company's EORI number for the import.
If that had been provided then we would have automatically produced a C79 Certificate.This is an import Certificate which allows the company to recover the VAT as input tax on their VAT return.
Please see the guidance below:
Check how to get your import VAT certificate (C79)
The shipping agent cannot raise a VAT invoice to the importer as the shipping agent is not making a taxable to the importer.
I would recommend the importer contacting the shipping agent to see if they can complete a post import ammendment.
Thank you.