Hello Minirunner,
SarahKelly is correct. If your ankle rolls daily during runs, it is so unstable that the ligaments are not being damaged anymore.
The clicking can be from a number of areas. Can you place your finger over the outside of the ankle whilst making circles and isolate the click. It could be from a peroneal tendon jumping across a bony point. If so, this may benefit from a tightening of the muscle, but sometimes surgery is required to ensure the tendon aligns properly without jumping.

If you have scottish, english, irish or scandinavian heritage you may have a gene that causes hyperflexibility of joints, predisposing you to problems. If you can bend your thumb back to touch your forearm, if your knees bend backwards more than most, if you have blonde or red hair and blue eyes you are in a higher risk category.

If none of the above applies, you may have a small piece of cartilage or bone that occasionally 'jams' the joint. You may require surgery (arthroscope) for this condition - scans first.

If you are lucky, then mobilisation of the lateral malleolus (outside ankle bone) posteriorly may increase the ankle mortice spacing which would improve movement. Of course, crepitus may be indicating ankle joint cartilage degradation, ie early arthritis.
Whatever the cause, you would be best seeing a sports therapist or ankle surgeon for examination and opinion.
Hope the above helps.
Cheers,
MrPhysio+