Why does God let bad guys exist?

Let me use this example from the Matrix Reloaded. Neo, Morpheus, and the Keymaker were going to open this door that would have exploded the whole building they were in because Trinity didn't shut down the backup generator yet. No one could communicate because Neo was in some backdoor portal thing. So Agent Smith shows up to fight Neo, Morpheus, and the Keymaker to delay them long enough for Trinity to shut down the backup generator, then Neo, Morpheus, and the Keymaker opened the door just in time.

So in this case, Agent Smith played his purpose to perfect God's timing and plan.

https://www.youtube.com/watch?v=7UigTsW0ZVE