what does this warning message mean?

[ntnik]

"There is a circular chain of references among the highlighted elements."

encountered when cutting a dormer opening in the roof (all cutting surfaces are selected then i get the warning).

[sbrown]

It means that a line, wall or other ref. used to create one object is then being used to create another which isn't allowed by revit. So in your condition you need to see what common element is being used to define both the roof and the dormer opening where if one were deleted it would effect the other.