I'll take a guess but could be right, I'll explain now.

The upgrade happens systematically, and per module...

It could still be in progress. Please share the last bit of entries of the upgrade log which is in Public_html/logs folder.

I won't really recommend a live site to be on auto or forced upgrade by default, hence will you use this feature. Run the upgrade on your dev box first, always.

Also, switch on automatic update maybe on a Friday afternoon, when production hours are not that much compromised, but on Dev, keep it always on, to keep up "what happens behind the scene"

To conclude, always check if there are any update in the AppStore after an upgrade.

(The above might not be on point, but a rather close speculation if one tries to figure out.)