Having a look at the exported FBX file it looks like the extra bones are being added by the pose.
Pose: "Pose::BIND_POSES", "BindPose" {
Type: "BindPose"
Version: 100
Properties60: {
}
NbPoseNodes: 38
PoseNode: {
Node: "Model::WORLD_center"
Matrix: 1.000000000000000,0.000000000000000,0.000000000000000,0.000000000000000,0.000000000000000,1.000000000000000,0.000000000000000,0.000000000000000,0.000000000000000,0.000000000000000,1.000000000000000,0.000000000000000,0.000000000000000,0.000000000000000,0.000000000000000,1.000000000000000
}
PoseNode: {
Node: "Model::WORLD_center"
Matrix: -1.000000000000000,0.000000000000000,0.000000087422777,0.000000000000000,0.000000087422777,-0.000000043711388,1.000000000000000,0.000000000000000,0.000000000000004,1.000000000000000,0.000000043711388,0.000000000000000,0.000000000000000,0.000000000000000,0.000000000000000,1.000000000000000
}
PoseNode: {
Node: "Model::MilkShape3D Object"
Matrix: 1.000000000000000,0.000000000000000,0.000000000000000,0.000000000000000,0.000000000000000,-0.000000043711388,1.000000000000000,0.000000000000000,0.000000000000000,-1.000000000000000,-0.000000043711388,0.000000000000000,0.000000000000000,0.000000000000000,0.000000000000000,1.000000000000000
}
PoseNode: {
Node: "Model::Cabin door01"
Matrix: 1.000000000000000,-0.000000079546602,0.000000026051277,0.000000000000000,-0.000000080342978,-0.819814205169678,0.572629690170288,0.000000000000000,-0.000000025136902,-0.572629630565643,-0.819814264774323,0.000000000000000,29.966440200805664,-21.186544418334961,19.161058425903320,1.000000000000000
}
PoseNode: {
Node: "Model::Cabin door02"
Matrix: 1.000000000000000,-0.000000080821508,-0.000000022329665,0.000000000000000,-0.000000079649460,-0.848980665206909,-0.528423905372620,0.000000000000000,0.000000022742583,0.528423905372620,-0.848980665206909,0.000000000000000,29.954044342041016,21.722658157348633,18.635986328125000,1.000000000000000
}
PoseNode: {
Node: "Model::WORLD_center_0"
Matrix: -0.000000043711388,1.000000000000000,0.000000000000000,0.000000000000000,-1.000000000000000,-0.000000043711388,0.000000000000000,0.000000000000000,0.000000000000000,0.000000000000000,1.000000000000000,0.000000000000000,0.000000000000000,0.000000000000000,0.000000000000000,1.000000000000000
}
PoseNode: {
Node: "Model::Airplane tail"
Matrix: -0.000000044659320,0.000000313913773,-1.000000000000000,0.000000000000000,-1.000000000000000,0.000000476839887,0.000000044659330,0.000000000000000,0.000000476839887,1.000000000000000,0.000000313913745,0.000000000000000,115.996002197265620,-0.000005137659173,-7.459563255310059,1.000000000000000
}
As you can see WORLD_center is there 3 times plus the old milkshape one.
You can see this when you compare gr2 files.