I found this out in this specific spot on the world seed 6829203619343862041 (generated in 1.13), I don't know if this issue applies in any other situation on any other world or any other place in this same world.  This issue was first discovered on this world on our server I was playing on and of course I went and tested it in Singleplayer and the same issue happened in the same spot. So to get the exact spot this issue is located at do: /tp @p 1763 72 255 without moving your character do /fill ~ ~-1 ~ ~30 ~-9 ~-30 minecraft:air you will fall down a few blocks and uncover the ravine for easy visual testing.

So then I use this command to fill the top three layers of the ravine's minecraft:air blocks with minecraft:grass_block blocks: /fill ~ ~-1 ~ ~30 ~-3 ~-30 minecraft:grass_block replace minecraft:air  I get a message that it successfully filled  ONLY 4 blocks and that's it.

So then as a test I used a similar command to remove the minecraft:stone around the natural ravine and replace it with minecraft:air with this command (again without moving the character): /fill ~ ~-1 ~ ~30 ~-3 ~-30 minecraft:air replace minecraft:stone  It will remove the stone as intended and fill with minecraft:air.  Then I used the command to replace the minecraft:air with minecraft:stone again with this command: /fill ~ ~-1 ~ ~30 ~-3 ~-30 minecraft:stone replace minecraft:air And with that command being used none of the ravine's minecraft:air blocks are replaced with minecraft:stone blocks as expected, only my minecraft:air blocks that I created previously are replaced successfully. **

Here is a video to showcase from beginning to end exactly what happens by doing exactly what I typed out here in this report, from beginning to end.  https://www.youtube.com/watch?v=0XWFKOTF_Yg