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.
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
Did anyone else in your fire team get it?