I'm experiencing this on one of my web properties since around the 8-9 of May.
One domain is named with the format: bookings.example.com
The other domain is named with format: payments.bookings.example.com
So everything is going to the same tLD.
GA Universal tag is injected through GTM, using cookie domain "auto".
I'm trying different things locally on my machine, and even using the standard analytics.js code, I'm experiencing the same issue.
Anyone else? Is Google having issues on the back-end, or did something change in the way sub-domain tracking works?
It looks like if you use the original ga.js code and have your tLD in the _setDomainName, subdomain tracking works properly.
However, if you use analytics.js by itself, or through GTM, and use "auto" for the cookie domain, you have to put the tLD in the Referral Exclusion List, even though the _ga cookie is properly set identically across sub-domains, and tracking should not (you would think) consider the sub-domains as referrers (especially since I could not find anything in the GA doc that says you have to do this).
I had initially put the tLD in the list for a completely different reason (for cross-domain tracking from ccTLDs to the .com and back), and probably removed it when I was testing another solution a couple of weeks ago... but since History Change doesn't show any of these changes, I can't be sure.
It's always live and learn with GA/GTM: documentation wise, it's quite poor. Granted it's improved a lot since the early days, but it still has quite a way to go.