Edit: I was definitely thinking of the wrong chests because of the previous quest stage, thanks everyone!
I'm in Step 3 in "Trust Goes Both Ways" and I've collected every faction chest in the Miasma, but it only says I have 1/4. I believe this was because I collected these chests [i]before[/i] I had got to this step, which makes this impossible to progress.
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Throw on a chest finder mod on your ghost, quest wll take a few minutes to complete.