Just had this happen to me doing a Legendary Wellspring as well. After killing the boss, there were small amounts of glimmer still counting down, much like when starting the second encounter, where you cannot access the rally banner. No rewards dropped, and when checking the Map director, the gold star for a pinnacle was still showing as if I never took part in the encounter. At least I may have the opportunity to run the activity again but these types of bugs are increasing.