God has a sense of humor. I always get a good laugh at this expression, as I'm sure God does, too. Actually, what is meant by this expression is that God is not doing things the way we want Him to do them. Now certain intentions in prayer are definitely God's Will, as, for example, the salvation of a person. But some things we pray for may not be for our good or the good of others.
Parents say it all the time to their children.
The apostles and others were wondering why Jesus hadn't come to cure His friend Lazarus before He died. One thing we need to always keep in mind is that whatever God does He does for our good.