There are reasons that i found here on the forums, but remember, bungie did not make a statement for this problem. 1) lag. If your team got rewards but you had lag at that time, the game thinks you didnt beaten it. If you were solo, atheon or crota would appear out of nowhere again and most likely kill you. 2) you already completed it. 3) because during the boss fight, you switched characters/team members and it counted you as a 7th persons, only 6 get loot. 4) server problems. You cant do anything and its up to bungie. 5) combination of both lag and server problem. Meaning lag tells the game too late that you beaten it, and server cant correct this fast enough. There are some more that i quickly need to find again but i will edit them in. Basicly, fastest way to check is to load it up again. If you have the atheon checkpoint, you didnt completed it. Also with the app. Select the character you did it with and look under advisors. If VoG is yellow you completed it. If you only did atheon, only one bar will be there tho. Not sure if gatekeeper and atheon share a bar. Hope this helps you a little. Atleast to find out if it was lag or server problems. It also could be a combination of both.

Remember, you can only complete it once a week. Otherwise, i have no clue.