Ok, that makes it a bit clearer.
IITC is no longer syncing with Pokemon GO or the Wayfarer database as previously known. The announcement is found here: Important Updates Regarding Wayfarer and Ingress . So these wayspots you see in this map may not be up to date with the game of choice.
What could’ve happened can be one of these scenarios:
- The missing wayspots is still in the Wayfarer database on an occupied cell.
- The missing wayspots were removed from the database entirely.
What I can recommend you to do is
Go onsite, check your submission map for orange pins 
denoting that the wayspot is still in the database.
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If it still exists in the database and find that the pins are misplaced from the actual locations (not the cells), you can put forward location edits via the help chat bubble on the Wayfarer website. Note the clarification for athletic fields:
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If it still exists in the database and find that the pins are accurately placed, there is nothing to do even if the cells do not work in your favor.
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If the wayspots are not found in the database, you can lodge a restoration appeal following the format in Wayspot Appeals .
In cases where you would need to do a restoration appeal or a location edit, geotagged photos are handy evidence that the object still exists at the time of the request. You may need it for the mural especially.