I opened up my model today and the skin weights were spotty and all over the place. When I closed out of the program last the skin weights were fine and I got no errors. When I go in to edit them they won't edit and put weights in weird spots on the model. Ex: Trying to put weights on the left hip and the weights are showing up spotty in the chest area. I have both the joint and the mesh selected but I'm still learning Maya so I don't know if it is an error on my end or a glitch.
The problem might be that the joint itself is too large. When you select them separately, the joint is a sphere you're trying to paint across and the difference in the objects is creating some complicated hidden geometry.
You could try:
Reducing the size of your weight brush.
Reducing joint size.
Binding your Mesh and Joints, repaint.
If none of these help, if you could send some screenshots of your process I could help further.