Editor keeps popping up with "This level has been edited outside of the editor"

how do i fix this?

Hard to say since you provide basically zero information.

When does this happen, while playing ? Is it an edited map or not ? Is it a mod or not ?

Assuming this is the vanilla, unedited map, I’d say verify your game files.

This is a known issue with the editor, not sure there is a fix. Used to see this all the time for other modders, if anyone figured out how to fix it they never shared how.

Given that the modding tools are also the ones Crate has been using, should they not know how to prevent / fix this? Maybe they can share some best practices to avoid this.