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Walking through ghosts sometimes caused them to be deleted. See https://youtu.be/JyHcNsMzwlE

Note: Video shows only solar panels deleting, later observed other entities too.

Log file: https://pastebin.com/vjs7EWji

Save attached.

Maybe ~1000 ghosts or so on the map.
Seemed to stop after a while or by walking through a ghost of another object, then starting again shortly after.

This is actually not bug of Factorio.

The mod Induction Charging is creating entity called induction-shadow on the location of the player.
This entity is specified in a way, that it would collide with the entity, so it triggers removal of the ghost.
Adjusting collision mask of the induction-shadow entity in the mod should prevent the issue.