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 ?

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The film's official novelisation indicates that there were, at the time that Yoda and Obi-Wan infiltrated the temple, thousands of armed clone troopers on site, facing regular attacks from various Jedi still in hiding.

Thousands of clone troops swarmed the Jedi Temple. Multiple battalions on each level were not just an occupying force, but engaged in the long, painstaking process of preparing dead bodies for positive identification. The Jedi dead were to be tallied against the rolls maintained in the Temple archives; the clone dead would be cross-checked with regimental rosters. All the dead had to be accounted for.

This was turning out to be somewhat more complicated than the clone officers had expected. Though the fighting had ended hours ago, troopers kept turning up missing. Usually small patrolling squads-five troopers or less-that still made random sweeps through the Temple hallways, checking every door and window, every desk and every closet.

Star Wars Episode III: Revenge of the Sith - Official Novelisation

It's not especially clear whether the troopers at the front entrance had been noticed missing yet but even if they had been, a Jedi going into the Temple wouldn't have been the troopers first guess. They'd be more interested in Jedi inside escaping.

  • +1 for Master of Novelizations :) But it is still unclear why Yoda and Obi-Wan didn't encounter any of those thousands of Clones collecting bodies inside the Temple.
    – rs.29
    Oct 8, 2017 at 19:59
  • 1
    @rs.29 - It's almost like they have some sort of magical power that helps them to avoid the clone troopers.
    – Valorum
    Oct 8, 2017 at 20:11
  • Yes, this power works on all Clones, except on those guarding the entrance. Entrance is anti-magical :P
    – rs.29
    Oct 9, 2017 at 17:18

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