Did you hide or delete (or add ?) some of the Nodes / Bones from the scene ?
I.g. you get this when the object hierarchy in your exported file is different from the one you are merging to.
Might be some setting of the ex- (or im-) -porter making it to skip certain stuff.
If everything else fails - the issue can be fixed in NifScope, by taking apart the hierarchy in the exported file and i.e. removing the offending node - but it's some trial and error, as most of the time you don't really know which one it is.
Make copy of a file you just exported, then go and try deleting (just "delete", not "delete branch") some nodes, so the mesh node will "drop out" from the hierarchy. Then try copy/paste it into the target file again.
The SceneRoot and/or the parent node of the mesh are best candidates for deleting. Don't delete any bones.