The President’s opponents played the electorate like a fiddle and will get away with it because people don’t seem to realize they’ve been tricked into being angry at the wrong person.

The only way he could have stopped these sections from being included would have been to try to veto the bill in its entirety, a move that would have been both political suicide as well as being futile, as Congress would simply have overridden him. He is explicit in his opposition to exactly the parts of the bill everyone here hates, going so far as to detail exactly which sections he opposes and why.
You’ll notice that the bill also restricts his ability to close Guantanamo Bay; this isn’t coincidence. These sections are openly hostile to the President’s stated mandate – they are effectively a giant ‘fuck you’ to the President, as well as a nasty way of eroding the President’s support with his own base.