It's a result of this change, which made the upgrade keyboard hotkey work for successive upgrades.
My knee-jerk reaction is to just say "well, don't press the upgrade hotkey twice if you don't want to upgrade a structure twice", but obviously not everybody plays like me.
Changing the hotkey behavior via a settings entry doesn't seem like a good solution, but adding another "single-upgrade" hotkey may be reasonable.
@Jip Thoughts?