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Once I sent a wayspot nomination but it was rejected due to poor picture quality. But when I was adding another wayspot through Pokémon GO it was on map and was use in other niantic games. But it also not appeared in ingress.
Each game has its own inclusion rules. It's possible for wayspots to meet none of the inclusion rules for any of the games and thus end up solely in the Lightship database.
Someone else probably submitted it and it was accepted when they submitted it, but reviewers didn't like your photo when you tried to nominate it, so rather than mark it as a duplicate, they rejected the picture.
That can happen. It may have been rejected before reviewers got to the duplicates check.
As for already being on the map, it can happen too, as it’s added to Lightship firstly and then to other games if it meets their rules for inclusion. It might appear in another Niantic game in future.