He could have but he'd have to veto the entire budget bill. He can't veto a part of it. If he had, the budget would have run out and we'd have another government shutdown. It sounds like he worked a deal. He signed the bill to avoid the shutdown but congress agreed to debate it further.

“In a time of deceit telling the truth is a revolutionary act.”
― George Orwell

It's not over when you lose. It's over when you quit.