Thank you and i want to add that Ragdoll Dynamics is just what i have been looking for years.
As you said in the chat; it did happen after assigning any bone in a armature and then duplicating a bone (any bone, not necessarily the assigned one) that existed before the assignment.
It is not a problem if you take it into consideration, a bone created after the assignment can be duplicated and mirrored before any new assignment.
I stumbled into this after assigning a segment of a armature for testing before i finished mirroring the hand. Believing the "delete all physics button’ in system would delete all the markers on the armature but it seems to keep the bones id’s in memory so once i tried to apply the markers on the mirrored hand it gave the .R bones of the hand the same marker as the .L.
It is not a problem if you work with a finished rig, but there was no mention of this (as far as i have read, sorry if missed it) and i guess there is people like me who could stumble into this without realizing.
note 1: the segment of the armature i tested wasn’t the hand or the arm as far as i remember, this is why i was really confused when the hand kept giving me this problem.
note 2: I’m not sure if the screenshots are needed as i feel i did a fine attempt at describing it in text. I hope this helps in some way.