I just lost most of a day to this very problem and am stuck with trying to find a fix. Using Import[], Mathematica 10.2 reorders the vertices of both binary and ascii input files PLY format, whereas Mathematica 9 preserved the order in the file. This is enormously problematic for me, because like many people I work on these geometry files in other software as well. Maintaining the vertex order is critical to this workflow. I presume that the reordering was added to obtain some optimization in rendering or retrieval of the MeshRegion object, because a ply file saved from Mathematica does not appear to be reordered again on import. Can we get an element added to retrieve the original vertex order, or an option to prevent the reordering on import?

Does it result in the same MeshRegion object.

How are you importing the list of vertices? Are you using Import[..., "VertexData"] or looking at the resulting MeshRegion in someway?

Either of them don't seem to have any guarantee that they give the vertices in the order listed in the source file. So it's not a bug by itself.