Cross User Directory Operation Not Possible
Adding an LDAP user in a child group of a nested group in Internal directory wouldn't let him inherit the parent group membership. On the contrary, adding an internal (local) user in the child group of the Internal nested group automatically makes that user inherit the parent group membership.
The user account used to setup the nested groups belongs to the JIRA Internal. The cross user directory operation is not possible but in case that some groups are duplicated, this might be just a confusion rather than an issue.
Check with the customer, which user account was he using during the nested group settings. Is this user account belong to AD user directory or Internal user directory? You have to create a user from Active Directory with admin access so that he would be able to manage LDAP users and the nested groups settings would be applied. JIRA and LDAP are two different applications even you have integrated LDAP to JIRA, still it requires separate admin users who can manage each directory.