We just pushed out a patch to help with a number of issues, but one of the important ones is described here: http://www.bungie.net/7_Bungie-help-I-finished-the-Raid-and-the-boss-didnt/en/Help/Article/12167
If you are seeing similar issues in the raid after taking the patch please post them in this thread and we'll investigate.
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[b]There still seems to be some confusion, so let me restate this clearly:[/b] Defeating Atheon gives you a [i]chance[/i] to get Raid-specific Legendary items, but there are [u]no[/u] guaranteed items that are awarded. You may get completely different items than your party members. The rewards for killing Atheon and completing the Raid are awarded when he dies. For this, you will receive rewards from Atheon's Loot table or at the very least, Ascendant Materials. There is no post-game screen that shows all the gear and loot that were earned in the Raid.