Why is EA calculating VAT on the whole amount of my purchase invoice with uplift?

When adding an uplift to a purchase invoice, why is Expert Agent calculating VAT on the whole amount rather than just my uplift portion, whether the contractor is VAT registered or not?  

As you are adding an uplift to the contractor’s original invoice you are essentially taking responsibility for the contractors invoice and then billing the Landlord separately. This is no longer seen by HMRC as a disbursement and so if you are VAT registered, VAT will need to be charged on the entire invoice rather than just the uplift portion. Please see this page from the Gov.uk website for further details.