Welcome to the forum!
The phrasing “used in other Niantic games” is poor, if you are talking about the wayspots you see as exclamation points on the nomination map screen in Pokemon Go. It should say “Wayspot not used as a Pokestop or gym”.
The email tells you “Remember that not all accepted nominations will appear in all Niantic games”. This topic should help explain which are used:
If you would like a visual of your situation after reading that, you can leave the gps coordinates and someone should be able to show you.