I have 3 examples of players that I face every day and that after becoming inactive, last thing they did was an upgrade and at the day today it is still not finish.
The examples are:
Nevermind: 3 sheep barn lvl8 and 1 gold mine lvl8
Bluuer: 1 sheep barn lvl9
Riansa: Cooper lvl4, Cooper lvl3
My guess is that they uninstall the application or lost their phone with account. So the upgrade is sort of tied to the client app to finish. I notice that when I speed up any upgrade with pearls, I still get the notification when the normal time is over about the upgrade is completed. So I think it is the app finishing the upgrade to the server.
Suggestion: Run a process that finish this upgrades often