1] Rental car companies do not just deliver a car and then leave their rental agent standing in the parking lot while you drive off. One of the subplots that I think is supposed to be funny is about these two priests who can't go on a road trip because car won't start. They call a rental agency which, instead of picking them up and bringing them to the lot, just sends an agent over in their rental car. And then he just gets out of the car as if they'll drive off and he'll sit in the church parking lot until they get back.
2] Not every atheist is literally a murderer. This one's pretty subtle, but if you watch closely you'll notice.
3] During the classroom scenes, all the students with laptops used them exclusively for taking notes. Not one of them was looking at Facebook. That would be such a cute world if it existed!
4] Not every atheist will break up with his girlfriend because she got cancer. Another subtle one, but if you pay careful attention to the movie you'll see it.
5] Philosophy classes usually involve actual philosophy. On day one of the introductory class in the movie, there's no syllabus or introduction. The professor just tells everybody to sign a piece of paper saying God is Dead and then class dismissed. Even psychology classes aren't that easy.
6] Not every atheist is a racial stereotype who's one lecture away from becoming Christian. They try to sneak that one by you too.
7] During a rock concert it an arena, people can't just have conversations. Music is loud.
8] Not every atheist is verbally abusive to his dying mother, calls his wife stupid at dinner parties, or hits his daughter. Again, they're really subtle with the way they portray non-Christians.
9] If you group text everybody in your contacts list the phrase "God's Not Dead", you will not be helping your cause. You'll be the biggest asshole in the history of phones.