The new replica contains the ACL of the source server but you did not copy the ACL

A replica stub is an empty replica that has not yet been populated with documents. When you choose File - Replication - New Replica, Notes® creates a replica stub and populates it with documents, either immediately or at the next scheduled replication, depending on the option you select.

Somebody modified the access control list on the source server before initial replication occurred

If you create a replica stub and somebody modifies the ACL on the source server before initial replication occurs, the ACL on the source server becomes the most recent one and replicates to the replica stub. Simply opening the Access Control List dialog box on the source server replica and then closing it can cause this problem.

The server times are not synchronized

If you create a complete replica immediately (rather than creating a replica stub) and the time on the source server is later than the time on the destination server, the new replica contains the ACL from the source server.