Thesis: Miracles actually takes place in the same universe as Angel and the events of Angel explain the strange phenomena seen in Miracles.
In Miracles 1x01, Alva says that the paranormal phenomena “seem to suggest a large event is coming”. This event is the birth of Jasmine. The paranormal phenomena are probably a side effect of her coming down to Earth — moving down from a higher plane is probably a big deal and it makes sense that it would cause some weird things to happen on Earth.
In Miracles 1x06, the last aired episode, we learn most people have seen “God is Nowhere”. These people are called The Darkness and they’ll work together to do something bad. However, two have seen “God is Now Here” and God wants them to exterminate The Darkness.
The most likely interpretation is that the people who see “God is Nowhere” are like the people who have been “infected” with Jasmine or Cordy’s blood — they see Jasmine’s true face (she is not really God — God is nowhere) and will work together to stop her. The people who see “God is Now Here” will be loyal to Jasmine and must kill those infected.
The boy who murders the infected says that God talks to him in his head. We’ve seen (e.g. Angel 4x14) that Evil Cordy has the power to talk to people in this way with a loud booming voice that could easily be mistaken for God. This makes sense: Evil Cordy needs to kill off any who will ruin Jasmine’s work, so she gets the boy to do her work for him.
Furthermore, the timing is perfect. Just after that Miracles 1x06 aired, Angel 1x17 aired, in which Evil Cordy again convinces a young boy (Connor) to murder an innocent person so that Jasmine can be born. Then the Jasmine storyline plays out explaining everything.
There are additional hints that the shows are connected: The scene in Miracles 1x06 where Paul (the main character) imagines strangling someone severely in the ICU with a pillow is a lot like one in Angel 3x17 where Angel (the main character) strangles Wesley in the ICU with a pillow. And in Angel 4x21 a Church sign reads "God is nowhere. Jasmine is the way."