When a user receives an invite to create an account and the top User Directory in Confluence is an Internal with LDAP Authentication, they are still asked to set a username and password. If they set a username that is not in LDAP, they will not be able to log in. Also, the password they set is ignored as authentication goes directly to LDAP.

Setup:
First directory: Internal with LDAP Authentication
Second directory: Confluence Internal Directory
Copy user on first login not checked.

Send a user an invite link from Confluence Admin >> Users >> Invite tab. They will be prompted to set their username and password.

A better way to handle the invite would be to have a different signup page if the top directory is delegating authentication that simply asks for their email or LDAP username and pull the rest of the information from LDAP after a lookup.