You're able to type:
/fill x1 y1 z1 x2 y2 z2 minecraft:command_block 0 replace minecraft:stone

but when you add a datatag, it goes horribly wrong:
/fill x1 y1 z1 x2 y2 z2 minecraft:command_block 0 replace

minecraft:stone

though you can do this when you replace all the blocks like so:
/fill x1 y1 z1 x2 y2 z2 minecraft:command_block 0 replace

or
/fill x1 y1 z1 x2 y2 z2 minecraft:command_block 0 keep

but when adding a replacement block to it, will make the command incorrect due a bug in the parsing of the brackets. This is the error log of the command:
[20:57:15] Data tag parsing failed: Unbalanced curly brackets {}: Command:"/say hey"} minecraft:ston

There is no fix to this, that's why i'm doing it alternatively using the "keep" block-handling and change the air into something else, though that uses an extra commandblock