Deep Clone for Jira has to be granted specific project permissions to properly clone issues.
All necessary permissions are granted by default and no action is required if the default Jira permissions were not changed, i.e. the atlassian-addons-project-access was not removed.
If you manually edited and revoked necessary project permissions in a company-managed project, some features might not work, and a warning message will be shown. This can be fixed by managing project permissions as follows:
Navigate to the company-managed project you wish to clone issues to