I have gone to all nine 10 times or so, only the first time did they show up.
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I also have this problem. I received triumph for getting all9 yet, my quest says only 8/9.
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Destiny thinks I didn't get Entropic Shards #2 [spoiler]Asteryon Abyss, Concealed Void LS Ceiling [/spoiler] This is one of the 5 I got first for the first quest to destroy them. I got the last 4 and yet Destiny thinks I didn't, but they are all destroyed and gone. The worst part is anyone suffering from this bug will loose out on all their characters since they are tied together. Even if I chose to delete one of my characters and loose out on years of questing, it wouldn't matter since they are all tied together. This is a major bug and many people are just being ignored or told they are missing it. I would post a picture, but I don't know how to do that safely.