It turns out the Endgame Mission drops have had a bug, which referred the loot to a wrong weapons table.
Today around noon our time, we will deploy a hotfix for this, after which you should see:
1) Stage three challenge loot dropping weapons with a 50%, armor with a 25% chance and pets with a 15% chance and clothing with a 10% chance.
The next challenge missions (featuring new weapon variations again) is also in the works!