- Select the object
- Go to Edit mode
- On the Properties panel (change one into Properties if you don't have it while keeping a 3D view panel), on the Object Data tab, go to "Vertex Groups".
- Be sure you have NO vertex selected by pressing A_key to select all, and pressing it again to unselect all.
- Now, for each vertex group:
- Select it and press "Select", and then hover over the 3D view panel, and press H_key. This will hide all vertices from that group. (The Outline "has" even a "hide" option, but it doesn't work for me, maybe it does for you and saves you work... if not, you'll have to use what I just said)
Every vertex that remains has no bone assigned. So either you do what I did and remember their positions and go to weight paint mode... OR you do the smart way and add them to a vertex group from there:
With those missing vertices still selected, on the Properties panel, click the Vertex Group you want to add them to, and click "Assign".
After you are done, use Alt+H_key to make all the hidden vertices visible again.
The following may just be me, or may be because I haven't experimented enough but here goes in case after all that you are still missing vertices:
HOWEVER, I noticed that maybe because of how Blender has different weights, that it seems only those on max weight (red on weight paint mode) are counted, so after this you may want to test your model on LoadBonesFormatSample.java from Bones's examples. Then, whatever is missing from there, you go to vertex paint mode to paint it for the corresponding bone.