Same problem I went through the guide three times, revisited each location three times, and now I know that I have all of them but it still says 43/45.
Bungie needs to fix this.
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I'm experiencing the same issue...43/45 and I'm very confident I got them all. Went through everything 4 times.
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I stuck at 43/45 too and I did all of them in one go with a list. I'm 99% positive the ones that didnt count for me are the two javelin ones in Glacial Drift