That is down to the import process, but you can apply vat code when entering expenses one by one manually.
Resolution for 'codes applied issue: 'No VAT codes applied on expenses' available: Yes.
The codes applied issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the codes applied issue yourself by looking for a resolution described in the article. If it is a complex codes applied issue or you are unable to solve the issue, you may contact us by clicking here or by using other codes applied support options.
For more information about resolving issues related to codes applied in Quickbooks/QBO or to get support for the issue 'No VAT codes applied on expenses', click the link below: