That part about God was a bit disturbing in my opinion as well. But if you will look closely, the way the white guy explained how these people got powers was like something he can't really describe to the newbies that's why he was like "whatever, just picture it like this..blah blah blah.. ok? got it? OK! moving on..." something like that.
But the wiriter could've wrote something else rather making God "un-omnipotent" to the eyes of the viewers.
He could've said like "God was just having fun and he makes us clean up his mess. It's like giving us collectors something to do".
Another thing I was confused about is when Jun Woo stopped the time, Sun Ah somehow experienced it 'again' as well. Remember she was about to take early off from her work and when she was about to go out she noticed the time stopped? So is it safe to say that ever since Sun Ah got tangled with Jun Woo's time, she's now involved with Jun Woo from that moment on? I wonder why, because if she is destined not to be affected with Jun Woo's power then she should've experience the time stopping (everytime Jun Woo uses his powers) ever since she was born, right? Why just now?