I deleted most things in a Tamriel cell then I put down a few buildings. When I run the game, there are two ore patches overlapping one building. On the CK, there's nothing in there and on the cell view, there's nothing besides trees, that building and a few other things, but no ore.

Why is it popping up in the game?

My guess is because in your save game, since the ore is an object that can be activated, that its now stored in your save game. Its whats called a 'dirty save game'.

You would have to have a save game that has never had that cell loaded into it.

Does this happen with all activatable things in Skyrim? In Oblivion it was just with doors, if I recall correctly

I don't know, I have not tested this extensively.

What I did in Fallout was to disable the objects instead of deleting them. That way they become 'disabled' in your game instead of just ghosting in your save game. I have no idea if that will help in Skyrim.

I find it best to find a place that you do not have to delete or remove or change the location you are planning on using. Less headaches that way and its not really that hard to do.

Yep, that seemed to be the problem. Going to the cell with coc from the menu doesn't show this problem, it's only when I load a game.

Set PlayerREF, found in (any) cell, as the enable parent of stuff you want gone, then tick the "Set Enable State to Opposite of Parent flag. That's how *Edit undeletes and it always works. Deleting stuff has always been and probably will always be a bad idea.