If you’ve used up your iCloud storage you should have been informed and not just shown the upgrade button. But the button by itself merely shows the way to buy (or buy more) iCloud storage. It isn’t necessarily related to the sync mismatch.
Is is possible you switched off Notes sync on any of your devices?
Does one of the devices have the complete repository of notes it should have, or do different devices have different files? If it’s the former, you could take steps to remove notes in the device with the incomplete quantity of notes, then re-sync, downloading the complete files from iCloud (which is the canonical repository). You can confirm the canonical list of files by logging into iCloud and looking at the web version of Notes to make sure.
First, my iCloud storage allotment has room left. I just checked and I have 6.65 free out of a 50GB tier.
Sorry I was not more specific about this point. Let me be more specific:
Apple Notes Content Agrees:
iPhone (latest iOS) iCloud.com
Apple Notes Content Agrees:
Local Macintosh 1 (v10.10.x)
Local Macintosh 2 (v10.11.x)
Apple Notes Content Does Not Agree:
iPhone (latest iOS) iCloud.com
Local Macintosh 1 (v10.10.x)
Local Macintosh 2 (v10.11.x)
Apple Notes iCloud Sync is verified enabled on all devices.
That said, I recently turned on an iPad Air that had been set to the side unused. The iPad Air is running the latest iOS (11.4.1). Below are screenshots of what I observed.
I believe I may have a solution and I will be following up to share my findings.