After playing around with your model, I have come to the conclusion that this is an effect of SketchUp’s close vertices tolerance. The original edge on the near side of your cross passes very close to the arc that defines the edge of the arm (within 0.2mm). I think that during the post-operation cleanup, the arc is “capturing” the edge and for some reason SketchUp is also softening it. With hidden lines turned on, I see the following:
The first two images are the top and bottom of the near edge before the subtract, and the second and third are after. See how the vertical edge has been replaced by two that go to the next vertices on the arc?
The really strange thing is that this happens even if I use the “Dave Method” of scaling up before doing the subtract. But, stranger still, everything works fine if I scale up and then use Intersect Faces with… instead of the solid tools subtract! We’ve always been told that the solid tools just automate what you can do manually with Intersect Faces, but that now seems to be false!
This leads me to suspect that the solid tools operates on the unscaled Definition regardless of how you may have scaled instances, and therefore is affected by small geometry issues even if you scale. It’s a matter of semantics whether that is a bug (incorrect result) or not (operating as designed - even though the design is flawed). I’d call it a bug, myself.