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Aren't clones supposed to not think?
Although Palpatine could not personally give the order to each commander, he spent some time contacting some of them before Order 66 was transmitted to the entire army. In the first minutes after the order, several members of the Jedi Council were killed: Plo Koon on Cato Neimoidia, killed by Captain Jag, Stass Allie on Salucame, killed by Commander Neyo, and Ki-Adi-Mundi on Mygeeto, who fell victim to Commander Bacara. On Utapau, Obi-Wan Kenobi rode a varactyl named Boga when Commander Cody executed the order and ordered the AT-TEs to open fire on the Jedi, but Kenobi was able to escape and leave the planet. Later, he met with Grand Master Yoda, who also avoided death on Kashyyyk, repelling the attack of Commander Gree.
As noted, not all clone soldiers obeyed Order 66. On Murkhan, Roan Shryne and Oli Starstone were saved by the clone commando soldier Climber, who first requested confirmation of the order, and upon receiving it, refused to side with the government against those he had been fighting alongside, feeling sympathy for the Jedi. As a result, he was severely punished. However, this is the only known case so far where a soldier disobeyed the order; in all other cases, clone commanders and ARC clones carried it out without question.
If all clones are the same, then why do I have a sense of humor?