You probably picked up some fragments on a different character. When you are in orbit, press the dreadnaught, it will show you how many you have on the bottom right of the screen. If its lower then 45 then like i said, you must have picked up a few on other characters. I had the same problem. Your best bet !!! Use this guide, Cope paste all the fragments on a notepad on a computer and go through each one again. https://www.reddit.com/r/DestinyTheGame/comments/3lb4oo/calcified_fragments_sorted_by_location_and_videos