Dont worry about it, chances are she ISNT pregnant, if you used a condom despite some getting, but got the morning after pill 3 hours later you havent anything to worry about!
If your gf is thinking about it alot and worrying about it she will probably be getting stressed out and this may be causing the stomach pains! She should have a period soon too because that is what the morning after pill does, it should usually come a week after, however if a girl is stressed and dwells on the worst case scenario it could delay it because of the stress!
Tell her not to worry and you shouldnt either! Chances are very very low!
Chin up!