When replacing Stone with Fill command, it also removes Diorite, Granite and Andesite

Are you adding the parameter to designate the stone variant to replace? Each of those is a variant of "stone" and without the parameter, all stone variants are selected.

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I honestly did not know that. Must be a Bedrock thing. I'm usually a Java player and this was the first time trying it on Bedrock.
My bad.

I did not add the parameter for stone, no.