Public URL Identifier, normal link~both and even links with index.php are working (ojs 3.1)

I use public url identifier and when i use it, my both links work. I just want the public url identifier linked to work and not the normal link with the article number .

Example (public url link) -
Normal link -
With index.php and normal -
With index.php with identifier -

When both are enabled, both get indexed in google scholar and my other plugins like comments also changes with links. Also i have used redirect method to remove index.php but they still work and even they get indexed in hoogle scholar. So everything gets screwed up. I just want one working link per article not four pls.