I too am having the missing 50th calcified fragment glitch. I had 49 with my warlock (YES, i made sure 49 were not spread out) and when i beat oryx challenge i did not get the 50th fragment in the game no shader. BUT bungie website and app shows I have all 50. PLease let me know what is going on.
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I also have the same problem everyone in my fireteam got the shader apart from me and i checked Destiny ghost tracker I have all 50 but the grimoire card insight isn't unlocked for me. It's really annoying because knowing bungie they won't fix it till the next event or DLC
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Did anyone else in your fire team get it?