In "The Bully," when SpongeBob says to Mrs. Puff, "Can I be in a different class?" she answers "Why?" which might mean she actually cares about him. But why wouldn't she be happy that SpongeBob wanted to be in a different class if she wanted him gone in the first place, first hinted in "No Free Rides" where Mrs. Puff said, "Okay SpongeBob, all you have to do to get your driver's license, and never have to come around here again - is write a ten word sentence on what you've learned."