My character is equipped in all rare or legendary gear, he has the challenge Geared For Battle completed, but Fully Equipped, the challenge for magic gear isn’t completed.
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I have the same problem 
Well over a year later, this is still a thing. I’m in all Legendary or greater, marked as “Not Started.”
I removed everything and put it back on, no change. Seems to be an ongoing issue with challenges in general. I’m not sure what other challenges I have that are bugged, this one just stood out to me because it was near the top of the list.