As far as I can tell, the time bug seems to be fixed in the latest update.
I regularly keep a record of all my upgrade times. In the past, the upgrades would finish late by like half-an-hour or more. However, the upgrades I started in the past few days are all finishing on time.
I have not looked at other things like hero recovery time, but I'd bet that's also fixed. I encourage others to do their own checking to see if I've got it wrong.

