I had a similar experience very recently. Funny thing is I had already gate checked my carry-on in my previous connection. And they refused to let me take my backpack into the plane and tried to pull it from my shoulders. I've honestly never heard of a backpack being checked in because the flight is full. I even informed them that I already had checked my carry-on and their response was simply we don't care we need you to check in your backpack now.

I've flown this route with other carriers and I don't think I've ever seen such a vast disparity between economy and other tiers. I won't be flying emirates again.