I need 2 or 3 calcified fragments on my Titan but in the Dreadnaught directory it says I only have 45.
Similarly it says 4/5 golden chests on Mars when I have actually collected all of them
Minor issue but annoying
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The Dreadnaught directory is always correct from my understanding. It is likely that you collected some fragments on a different character that your titan has not collected. If you go to Bungie.net (website, not the app), hover over My Legend, and then select Advisors you can see a checklist of which fragments you have/have not collected for each character. Going by your Grimoire or any tracker website is inaccurate because they count the fragments you have collected on all characters.