Hi Shaks, I have seen the same problem for a small number of mailboxes on v11 16.25. At the time of writing 16.51 is out and I cannot see any hotfixes that pinpoint resolution of this issue.
Was it ever resolved for you?
Error message [The account does not have permission to impersonate the requested user.] is usually reference to impersonation rights via EWS.
Ensure the steps to create an impersonation RoleGroup have been followed: http://documentation.commvault.com/commvault/v11_sp16/article?p=92403.htm
If this has been done and you are seeing the above errors on some users still, the issue might be related to throttling from Microsoft.