As the title says, when using a repeating command that replaces water with air, the water disappears but some manages to slip through when it should not. That water that slips through dissapears and reappears really fast. And when it manages to go outside of the boundary of the command it just continues as normal.

Here's a link, because it's pretty hard to explain: [epilepsy warning] https://youtu.be/LaIncVtnaEE