I don't think it's a bug that you get MCMMO from it.
While this is not my speaking department, I can second this. Skyblock doesn't prevent McMMO experience gains in any way (as far as I am aware), only the creative world does.
Also, blocks that are related to the Mining Skill (stone in this case) have to be naturally generated to give experience. Since lava and water mixing counts as natural generation when it comes to obsidian, I induct it is the same with stone under the same circumstances.