An object with an "internal" joint means that a joint has been grouped with the object. Sometimes when repeatedly clicking on a grouped object to select a joint for deletion, the group is "opened" (temporarily exploded to allow access to the internal elements of the group). Occasionally due to an obscure bug, deleting a joint in a group opened in this way shows the joint still existing as an internal element even after it has been deleted. The best cure is to explode the object with the internal joint and re-group the elements. If your model is complex with many physics joints it is normal to have groups which have "internal" joints and is nothing to worry about as long as the joint exists. For example in chain with many links, each link would have one joint on one side as an "internal" joint and the joint on the other side as a "connected" joint. Let me know if any of that helps. If it does not, you will have to provide further details of the problem or upload your model so that people here can better understand the problem and try and help you further.