Can't delete a few extraneous faces in my model

I’m editing a model that I imported as an STL, and I’m 99% finished with it, but somehow there are a few extraneous faces in my model that I cannot delete without also deleting attached faces that I want to keep.
59_am
Here’s how I made this:

  1. Imported the STL from Original Prusa i3 MK3 ENCLOSURE -Ikea Lack table - Prusa Research by cisardom - Thingiverse
  2. Deleted the parts I don’t want
  3. Magnified by 10x (to get around a common problem with SketchUp and tiny 3D models).
  4. Created a solid, and merged it with one of the models via Intersect Faces With Model.
  5. Deleted the faces I don’t want

Most of the unattached faces I could delete, but for some reason, these remaining ones are still part of the attached faces they came from. I tried drawing a line to separate the two faces, but it didn’t work.
Prusa_Enclosure_Bottom_Corners_Front_Slots.skp (300.4 KB)

You have several small errors around the place. Too late at night for me to explain how to fix them. Here they are fixed instead.
Prusa_Enclosure_Bottom_Corners_Front_SlotsBox.skp (314.4 KB)

Thank you very much. I would grateful if you could tell me how these particular faces didn’t have intersections in the first place.