Hmm yeah that's possible. I think it might happen if the size of the ore patch changes at all, and then you load the game after updating/change mods or the base game version. If that's still annoying I could look into fixing that, but it might be more difficult.
An alternative idea that might solve your problem: what if there was an option to automatically hide icons for patches that have entities built on/near them? Would that do what you want? Are you manually clearing tags on patches you already have miners on?