I entered the lost sector for yesterday, completed it and expected for the legendary to appear, but it didn't. it even said after completing that i unlocked the legendary lost sector version but the flag never appeared. i switched to my warlock and completed it without a problem, it's just on my hunter that it is not appearing.
I tried today's lost sector and the same thing is happening. it says that i've completed the normal version and that i've unlocked the legendary version, but the flag never appears no matter if i run the lost sector again, restart my game, or go to orbit. it works on my warlock and titan just fine.
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Your hunter is too low power to see the legendary/master flag.