unreasonable intersection lines

edit

Based on your follow-up video, I've re-hauled my previous pics and comments. The following is more focused on the specific areas you've highlighted.

Zoom in the problem area (before intersecting the entire model). I used SketchUp's tape measure to highlight the tiny azimuth difference between Surface 253 and Surface 343. I think this is the source of your issue. I think this pushes OpenStudio to recognize the vertex (joining both wall surfaces with the floor above) as being collinear - not good. Just like any tiny overlap between 2 surfaces, OpenStudio users should really try to avoid slight azimuth differences between connected surfaces. Both wall surfaces are outdoor-facing walls - you should be able to fix this using SketchUp.

Once intersected, I'm able to reproduce what you've shown in your video (i.e. tiny gap between newly-generated floor surfaces):

However, if I save the newly intersected model, then reopen using SketchUp:

The tiny gap between floor surfaces has been auto-corrected, assimilated with a larger surface. Yet this inadvertently ends up creating a cutout, which OpenStudio corrects by converting it to a (transparent) sub surface, illustrated here using the OpenStudio Application.

The intersected model would obviously need fixing. I strongly suggest you fix the initial issue, rather than try fixing an intersected model. My 2-cents.