Mark-Up entries can change the color of elements.
Also, if a View is placed on a Layout as a Drawing and a different Pen Set is assigned to that Drawing, that can also change colors.
Also, inverted elements may also be displayed with a different color defined by the "Use uniform color to highlight inverted elements" in the On-Screen Options page of the Work Environment Dialog. That you should see that there is something wrong with the 3D geometry of that Roof.
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