I know this is an old post, but this is exactly the same problem that I have on nearly any model that I import from an STL. It takes hours to fix and because of it I am seriously ready to ditch SU for Fusion.
It's NOT caused from bad geometry practices so don't even say it! I can have a hole in the mesh and literally draw 1 line to close it and it will create many extra faces. I have had up to 15 extra faces on top of each other! This is a serious bug and I cannot believe it is still going on many years later!
Most of the holes are caused when I import an STL into SU like I did with the example file that I am including. I have already painstakingly closed each hole up manually since I have yet to find an extension that can do this automatically. I bet I spend 50% of my total time in SU just fixing holes and deleting extra faces, this is simply unacceptable.
Please help if you know what is going on and how to fix it.
Thanks!
Run Solid Inspector to see all the extra faces