It seems your display mode is “Wireframe”. Try to change it to another one.(Shaded or whatever…)
And the result would be a mesh. Are you familiar with mesh?
It is because they are not flat. If you do not care about flatness, just use component from NGon called FromPolylines.
Or it is just tolerance issue.
Normally if you just cut pyramids with plane you will have a flat cut. But if those extrusions are not pyramids then they are not planar. The planarity is lost when polygon scaled.