Revealing mistake: When Stuart's dad is giving final instructions to Stuart as he's about to lower him down the drain, Stuart (and his bright yellow shirt) aren't reflected in the dad's glasses.
Revealing mistake: When Stuart falls in the garbage truck, the bag has a hole in it before he hits.
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.