I think I found the issue. Layer settings do not seem to carry over. In the top right of the inspector, click on the layers dropdown and create a layer. Click on the hips of the ragdoll model, then hold shift and click on the bottom body part in the heirarchy. Assign them all to the new layer. Now in project settings (edit -> project settings) click on the physics tab and scroll to the bottom to where you see the layer collision matrix. You will see a table of all of your layers. Make sure where your new layer meets with itself, the check box is unchecked. This will solve the issue. So sorry for the hassle! It took me forever to recreate this