After Order 66, Yoda and Obi-Wan returned to Jedi Temple and found it occupied by Clones. They do not try to sneak in, instead they openly attack and kill number of Clones. After that, they relatively leisurely investigate the scene, search for clues, re-calibrate message for remaining Jedi, watch holo-recordings etc ..
Since we know that Clone troopers do have communication equipment, it would be safe to assume they warned others that two Jedi are in the Temple (and they probably recognized Grand Master of the Order) and called for reinforcements. As no new Clones appear while Yoda and Obi-Wan stroll in the Temple, is it safe to assume that two Jedi temporarily captured whole Temple (or at least part of it) by eliminating all Clone troopers around ?