To reproduce:
1. Open attached project
2. Open scene MergeBug
3. Enter play mode - note that the character on the left is not animating (due to lines under !DoCombine in CombineMeshes.cs)

Explanation: In this case a whole new hierarchy with a new animator was created, while the animator from the original asset has been setup by the model importer to write into skin mesh matrix rather than transform which is not the case for a newly created animator, by default animator writes in to transform.