As children and as adults, Twilight always had conflicted views about her brother. Pure and simple, he was a weirdo around her. Sometimes, he would be in a good mood. Sometimes, he would be in a bad mood. And sometimes, he would be smarter than her using his strange logic. For Twilight, logic does not exist. Not that kind of logic. That logic was wrong because it always, always made her feel stupid.
Her brother Shining was aware of that and took pleasure in taking her down a notch. It's only a game that only smart ponies could understand... And if his sister couldn't understand that, she didn't deserve to call herself the smartest.