I had this issue as well. What I did was to uninstall all the Mods in the Content Manager. This left 5 "mods" that were not Steam Workshop mods. I suspect they may be the way C:S manages extra difficulty levels. They are as follows:

Hard Mode - More challenge for experienced players
Unlimited Money - Money Never runs out
Unlimited Oil and Ore - Oil and Ore are not reduced from terrain
Unlimited Soil - Landscaping without limits
Unlock all - Progression milestones are always unlocked

I DO NOT recommend uninstalling all the mods like I did!! :) Instead, sort the Mod List by author. This puts these mods at the top of the Mod List. Deselect the 5 mods.

That's it :) Good luck and build well!

Are you using Unlock All Unique Buildings by Bloody Penguin? That mod will unlock all milestones as well.

I had to figure that out the hard way because initially I just assumed it unlocked only unique buildings, but that's not the case. I was using that mod AND had the built in mod Unlock All enabled. So when I started a new game and decided to play my new neighborhood with everything locked, unchecking Unlock All made no difference. I wasted so many hours trying to hunt down a mod conflict that didn't exist.