In the Design File Cleanup tool within MicroStation CONNECT, sometimes I cannot properly delete all duplicate elements after selecting Apply.
Navigate to File>Restore Defaults within the Design File Cleanup tool to restore the default settings for this tool. Then see if your issue persists.
If this does not resolve your issue, try resetting your User Preferences and delete MicroStation's Temporary Files as described in this article.
Design File Cleanup
Remove duplicate elements