I have this same issue as well. I have found every fragment and still says 49/50. Hopefully Bungie will address this in time.
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I have fifty but didn't do the Eris quest lines after I did them she gave me the shader
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I have done everything for Eris and it still does nothing for me.
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Its bcuz if u use a website like destinycalcifiedfragmentfinder.com it registers every fragment u collect across all characters and if u have 49 on your main it means u collected the other on a different character, i have the same issue.
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I'll go through my main again for all the calcified fragment, but that's the only one I did collect them on. Thanks for the advice though