As soon as the arena resets, all of the rewards go directly into your account without your approval. So if you were at that point online, you would not get any pop-ups but the shards and gears would already be there. Most of the time that people report this kind of bug , they somehow pulled the shards already and then logged out. When they came back in, there was nothing left. 

If it's your case, then it's solved. If not pls send a ticket to customer support , and they'll check that once more.

In theory the problems with the arena chest will be fixed with tomorrow's patch