To reproduce:
1. Download attached project;
2. Open scene "Scene";
3. Select the 5 Cubes Mesh and note that it has 120 verts, 60 tris and 5 submeshes;
4. Select CombineMeshes in Hierarchy and enter Play Mode;
5. In inspector double click on the newly combined mesh in the MeshFilter and note that it has 600 verts, 60 tris

Actual result: A mesh verts are 5 times bigger than original.
Expected result: A mesh verts should be the same as originals, but with all submeshes merged into one.

Reproduced in : 5.4.4f1; 5.5.0f3; 5.6.0f2; 2017.1.0a5;