Currently it is not possible to differentiate issues which are cloned by using Jira clone feature (... >> Clone) and the issues which are linked manually while creating an issue using Cloners link type. For both cases, issue history shows the same data.

In some cases, It is essential to differentiate both operations because there could be integration/automation rule which is dependent on clone operations but when an user manually updates the cloner link type the integration/automation gets triggered without clone operation.

It will be good to have a JQL parameter or rest api data which differentiate both operations.