I have discovered that if I have mods in my game that doesn't apply to any type of building such as being able to purchase more of the in-game produce at the markets, and I have a garden in my lot that I'm uploaded it will show the lot as being modded, even though all the plants are from the game and not CC.
I have found the easiest way to get rid of the modded CC is to first build whatever, then save and exit my game. Then completely remove the mods folder, and then start up the game. After that go to the lot, and then upload it. It took me nearly a year to finally figure this out.