Maybe sq-footage has increased, but your data is about new housing across all economic classes and we are interested in median middle class housing. Besides the problem of data skew (richer people live in bigger houses), Warren claims that most of the middle class live in old homes, not new ones. She specifically says that new homes are being built for upper middle class and above.
It was median new housing developments. Not the housing of a median family, nor the housing of a median middle class family.
Again, Warren's claim is that median middle class families live in old homes. And even if they didn't median middle class homes are potentially smaller than median homes.