Same problem and solved. Ok so Bungie.net and not the app or phone. The go to progress. Select guardian. Then bounties and scroll down. All calcified fragments are shown.

Bump... 49/50 on my warlock, but as that one missing fragment was earned on another character, i don't know what I'm missing as neither my grim nor dcalcfrag.com can differentiate what class got what. Don't really have the time to go searching through all 50, y'all really need to fix this, or a bunch of us are gonna be screwed out of completion of mot2.