Hi,
You may want to confirm with the courier that the VAT not being charged by them is correct.
However, under the place of supply rules, if a UK courier were to charge for a freight service to a business customer based overseas, then this would be outside the scope of UK VAT and would be subject to the reverse charge by the business customer if they are based in the EU.
Therefore it is likely that the EU courier has deemed the place of supply to be in the UK, as that is where their business customer is based and so would be subject to the reverse charge by your company.
Place of supply of services (VAT Notice 741A)
Thank you.