Yes, I guess you could call it a user-error - at least in the sense that most people experiencing this are on custom ROMs with Gapps flashed on the top. Google apps and their proprietary libraries are somewhat complex in how they relate to account integration and future service updates.
The majority of the time, once a Gapps package is flashed on a device, that device should (theoretically) live in perfect harmony with the entire Google (Play) service ecosystem. They're meticulously assembled to implement everything smoothy, but sometimes, after Google makes a big change, things do not transition properly or cleanly.
In this case, Google made a fairly major change to it's messaging service, and the way it behaves in the background. Google Services Framework is a major part of connecting Google accounts with Google services, and simply clearing it can resolve most issues with syncing or sign-in. So yes, this could be considered user-error, even if only because stock devices were not affected in any significant numbers that I saw. It just happens, and nothing can be solved on Google's side. The ROM/root community seem to have been the main sufferers.