John Sides notes two recent examples (one from the UK, one from Putin's Russia) of how bureaucracy limits executive power. Nice catch!
Of course, Putin presumably had relatively few checks outside of the bureaucracy (warning: I'm not qualified to write about post-Soviet Russia). John Major's main checks (outside of the bureaucracy) came from his political party. Now, consider the President of the United States of America, who has to compete with a fully independent transformative legislature, independent courts, and independent state and local governments. Each of which compete with the president (and the bureaucrats themselves) in attempting to influence the bureaucracy. Add it all up, and there's just no way that we can assume that because the United States government does something, the president must have wanted it to happen. Even if, in public, he may say so.
I'll also take the opportunity to once again plug the best means to understanding these issues: the wonderful Yes, Minister.