Character mistake: When Stuart calls home from the pay phone he's talking into the wrong end of the phone.
Character mistake: In the football scene, when the kid boots the ball to George who is upfield, he then hits it at the other kid, who is also on his team. There are two problems here: 1) The original pass would have been offside, as you see the all of the other players are still charging up the pitch. 2) When George kicks the ball at the other boy's face, that would have been offside as well, for reasons that are stated above.
Answer: Probably because he could see that she was hurt at what she did and also because earlier in the movie, he said "When you're friends with Stuart Little, you're friends for life". Also if you wanna look at it another way, him helping her could be payback for her saving him from the sink. It's just a long term friendship they have.