This isn't anything wrong with your graphics card or ArcGIS Pro.
The polygons are "z-fighting" with the ground surface. This is expected, and you can repro in ArcScene even by stacking a world-extent polygon with extruded polys with a small extrusion value.
The graphics card can't decide which polygon is on top (ground or the extruded polys) when their values are very close to each other.
To prevent them from z-fighting, the polygons can be OFFSET from the "Ground" (using "relative to ground") by some amount. Alternatively you can add MORE extrusion to ensure that the polygons' tops are "Above ground".
Z-fighting is pretty well explained here if you're feeling like reading more about it: Z-fighting - Wikipedia, the free encyclopedia