How many draggable handles do you have? Can you show a screen shot of the puppet panel with that arm group selected, and the mesh view option turned on (switch at the bottom of the panel)?
When the mesh is turned on, you'll see _all_ handles on the current mesh (i.e. the mesh that the currently selected layer is part of). When the mesh is turned off, you'll only see handles placed directly on the selected group.
If every group has its Warp Independently option (crown) on, these are the same thing. When the crown is turned off for a group, its mesh is combined with its parent's mesh.
So, to see that extra handle _without_ turning on the mesh, you'd just have to select the group that contains that handle.
Note that individual (non-group) layers can't have their own handles.