Automatic App Updates not in the Background anymore since iOS 10
I think this may be happening to you for a number of reasons:


iOS 10 has determined that you do not use the updating apps at that time of day, so it is updating them during use to be more efficient
iOS may also have determined that this time of day and network are when you have the fastest connection. 
If you use Airplane Mode at night (for faster charging and no notifications), it can't update apps at night.
Or there's a software glitch.