I've seen this on other forums.  Yes, Intuit screwed up yet again and didn't do what is required.

I would reply to the IRS notice that it is a 100% charity, but your defective Intuit software did not include the required notation.  In that response, you can ask if they want an amended return, but I suspect that they will just fix it via that response.

The IRS is rather slow at responding, so expect it to take a long time to resolve.