Order 66 has traumatized all of us, which is why there are so many "AU order 66 never happened". We find the most ridiculous reasons to have the order simply never given in the first place, such as having Palpatine devoured by some Coruscant beast, which seems to be a favorite option among fanfiction writers.
But consider this, there's a very realistic reason for why many clones may not have responded to Palpatine's order, and that’s … brain damage.
No seriously, how many concussions would a normal clone who regularly goes into battle against droids made of iron carrying lethal weapons have received on a daily basis? (And let's not forget about the occasional sith who loves to throw people around with the Force).
Furthermore, their armor and helmet are almost always in poor conditions, and the Republic considers them expendable enough to never send enough new pieces to repair them nor enough medical supplies to actually treat their injuries, which means they are more vulnerable on the battlefield.
If we take into account battalions like the 501th or 212th, which seem dead set on fighting anything with their bare hands in case of lack of blasters, and are consequently thrown into the air or into any nearby rock like rag dolls on virtually every mission, it is not hard to imagine that their brains received a high enough dose of damage that the control chip can't work.
Especially because there are enough of them who decide they don't need a doctor simply for almost breaking their heads, and continue to accumulate concussions as if they were stamps.
The result is that when Palps gives the famous "Execute Order 66" in that dramatic and tense moment, expecting an immediate result, half of the clones go "????", not understanding what the hell the emperor is talking about. They don't even notice the physical effect of the chip malfunctioning, as they have been living with headaches and migraines for so long that the change only causes them a little discomfort.
The other half, who only have a partially damaged chip, manage to fight the urge to kill their Jedi long enough to be stopped by their brothers.
And this is how Palpatine's neglect of the physical condition of the clones backfires against him in the most spectacular way possible.
The genocide of the Jedi does not occur, especially because most of them, once they understand Palpatine's betrayal, backtrack at full speed towards the Temple, extremely pissed off and heavily armed clones in tow.
Anakin is knocked out when Obi Wan, Ashoka, Rex, the entirety of the 501th and a very pregnant Padme jump him at the same time and begin to hit him violently on the head, half convinced that he too is mentally controlled, and half because they believe that Anakin is stupid enough to have actually let himself be convinced by Palpatine to do all this of his own free will.
Palpatine tries to escape, but barely makes it out the senate door before Fox tackles him on the ground like a common criminal and fires a clean shot into his head. No one knows if the chip of the commander of the Coruscant guard didn't work due to numerous brain damages (very possible) or due to the quantity of caf he ingested being so high that he short-circuited the thing (hypothesis pleaded by his fellow corries), or due to a secret third explanation (It's this one, but Fox will never reveal it to anyone though).
No one else is there to hear when the commander, blaster pointed at the emperor's temple, says, "This is for Fives."
The catastrophe that would have started the empire is avoided, and once some fundamental changes within both the Senate of the Republic and the Temple (more precisely, the revision of some points of the Jedi code, as well as the establishment of mandatory therapy sessions for all Jedi Generals), millions of clones are forcibly dragged by their Jedi into the Med Bay.
Just because their brain damage helped save the Galaxy doesn't mean they can keep it.
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