Warning Message - Highlighted Elements are Joined but do not Intersect

Revit is telling you that someone used the Join Geometry feature on elements but now they no longer touch each other, intersect. When they were moved apart a warning appeared but the user didn't click Unjoin Elements (see image), they clicked OK so now Revit is keeping track of the joined relationship; doing what it was told to do.

If they/you/we do this enough we'll end up with a lot of warnings to review here.

You/they need to fix the problem, Unjoin the geometry, no warning anymore. The Warnings dialog even gives us a way to fix it, click Unjoin Elements. Fixing accumulated errors like this will improve performance. Please don't regard the warning as irrelevant, it's not!

Better still, avoid the problem in the first place, click Unjoin the first time the message appears instead.

Oh, I should also mention that clicking Unjoin Elements in the Warnings dialog does Unjoin them BUT it doesn't clear that warning from the list until you close the dialog and open it again. That's a little confusing.