Hi Doug,
I see what you mean, this came even from a site with 100% guaranteed printable files

The problem is that you have to check over and over before you print. Mostly I only see a problem after printing.
In S3D you see that there's only a problem when you check for manifolds.
For example, if I use Slicer for this STL, after loading I immediately get a message that slicing could give problems due to the non water tied edges.
But when I ignore that, this file is sliced correctly and printed correctly.
I think that there can be some improvements in a next version of S3D to overcome these problems.