If God can do anything can he make a mistake?

"Communism killed 100 million people."

Actually that number has been widely disputed, the "100 million people died under communism" meme came from a book called "The Black book of Communism" by Stephen Cortois, which incidently two of the contributors (Margolin and Weth) are highly critical of the claim:  Margolin and Werth felt that Courtois was "obsessed" with arriving at a total of 100 million killed which resulted in "sloppy and biased scholarship",[33] faulted him for exaggerating death tolls in specific countries[6][34]:194[35]:123 and rejected the comparison between Communism and Nazism.[3]

Now don't get me wrong, Stalin and Mao were brutal dictators that killed quite a few people, but the "100 million people" meme isn't based on vast historical consensus or anything.

But sake of argument let's say 100 million people did in fact die under atheist communist dictators (which is what you're referring to). This doesn't really help your case, these governments weren't killing people "in the name of atheism" and trying to promote rational thinking and skepticism (quite the opposite really) they were getting rid of any competing idealogies with the state (Stalin also didn't like liberal and conservative political parties).  Why do you think Stalin and Mao erected statues and paintings of themselves as essentially idols to worship? They weren't trying to get rid of dogmatic thinking (which is what religion essentially is) they just didn't want other dogma competing with theirs. So this "100 million people died" meme doesn't really help your case, quite the opposite, Stalin relied on the same tactics that religion does (dogmatism) to spread his influence.