It happens when you move the ragdoll foot gameobject. You can only rotate it. To move the collider, do it via collider.center. To fix your rig, right-click on PuppetMaster header, then select "Fix Muscle Positions" from the context menu. If your foot colliders end up offset, move the colliders, not the gameobject itself. Another option would be to parent a new empty gameobject to the foot and copy/paste the collider onto that. Then you can move that child object freely.
The next version of PuppetMaster forces the gameobects in place so it should not happen again.