The minor versions of a document are not deleted after passing through a workflow that includes a state with the entry action Delete Minor Versions.
Check the order of the workflow actions.
If a state change occurs prior to a Delete Minor Versions action to Set New Major Version, it does not delete the minor versions of the document.
Include both entry actions, Set New Major Version and Delete Minor Versions, in the same state in order for the minor versions to be deleted as expected.
Vault Help Documentation: Defining Document State Entry Actions