This seemed so bizarre, I had to research it. Best I can tell, it originates on Page 97 of the proposed bill: https://waysandmeansforms.house.gov/uploadedfiles/bill_text.....

(2) Section 132(j)(8) is amended by striking "which are not excludable from gross income under section 127".

I looked up the mentioned sections:

Section 132: https://www.law.cornell.edu/uscode/text/26/132

Section 127: https://www.law.cornell.edu/uscode/text/26/127

This does seem to be true.

But to be fair to the intent, these sections of the tax code are aimed at educational benefits provided by corporations, and there is not a specific clause in the proposed bill that is targeting graduate education. It seems like an oversight that PhD students are affected by this, or possibly there's a deeper nuance in the tax code that makes this irrelevant to educational institutions. Hopefully all of the attention this has received will result in clarification and amendment before approval.