By default SpecChecker checks against each element’s actual saved symbology, while ignoring how an element actually displays.
Let’s say you have a rule that rejects elements with color not equal to pink. You look at the elements, and they are displaying pink just as they should. No violation, right? Well.... take a look at the properties of one of those pink elements. What is the color? ByLevel. The ByLevel color may be pink, but that doesn’t mean the element color is pink. The color is ByLevel
If you are okay with the element being ByLevel and not pink, what you can do is tell SpecChecker to test against the elements displayed symbology, rather than the saved symbology.
Below are directions for saving that setting.
Now when you process your files, the elements with correctly displayed symbology will not be flagged as violations for their symbology.