If I read correctly, he did not veto on the grounds that there is a section specifically stating that US citizens are exempt from this.
Sec. 1031 (e) Authorities- Nothing in this section shall be construed to affect existing law or authorities, relating to the detention of United States citizens, lawful resident aliens of the United States or any other persons who are captured or arrested in the United States.
I could be wrong, but that's what looks like to me.