The JCM's on most figures will be Pre-transform morphs. Bad thing happen with the morph brush, especially the smooth on pre trans morphs.

Bend the joint to a Workable position. Save or at least remember this pose. Select any of the morphs on the body parts involved (NOT the BODY of the figure) On the context menu for the morphs choose Convert to Post Transform

Make your edits with morph brush

Be sure the figure is in the same pose as when you started Select one of the morpsh Conver to Pre-Transform.