The arms won't highlight in rigging

Sorry for the incredibly late reply!! But you were totally correct, I had but the left hand in the right hand folder, fixing this fixed the problem, thank you!!

Looking at the artwork closer, I think its the hands. I think you have some right hands in the left arm still. This frequently happens because you hide the alternate had positions, which means moving and editing etc in Photoshop/Illustrator is disabled. So when you move and reflect the hands, it can miss the hidden hands.

(See how the yellow rectangle goes to the very edge of the right hands? That is why I suspect this.)

This happens when there is discontinuous artwork. I suspect some of the right arm artwork snuck into your left arm layer. That is why the yellow rectangle goes so far over to the right arm. Because there is a gap in the artwork, it cannot work out a single line (a single mesh to be precise) around the artwork in the left arm layer. Gaps in the mesh are not supported.

There is a mesh icon at the bottom of the panel. It you enable it, you will see triangles all over the rectangle, which is bad. You need the mesh to track the left arm correctly, after which the triangles will only be in the desired area.

So go back to the artwork file, then try to work out if there is any unexpected artwork that should be outside the left arm layer (e.g. hide the other layers).