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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I just completed crota's end on normal, making sure to look on the Destiny app to see that I hadn't completed it yet. We killed crota, and I saw everyone on my team get their exotics and black hammers. I didn't get anything, not even shards. I looked at the app again, and it said I didn;t complete it.