I’ve been farming the Templar’s Chain and when a mysterious chest spawned finally spawned on Cathedral Lv2, it only had blue items (similar to issue with Liquid Rainbow not dropping)
Maybe try removing your pet when you open the chest if your altar allows the pet to pick up items.
I’m not sure how pets interact with these kinds of items.
There is a transmog that I really like, when I search for it, I always remove my pet for safety/caution (it’s a blue item)
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I’m not surprised. Once I unlock the Husk Seal my Pet will pick up and salvage Transmogs dropped in the Realms by the Uber Bosses. I’m sure there’s others they pick up too. But, I’ve never tried to document which ones they do or don’t. And, if I remember correctly, there are some I have been able to pick up.
So, when you find a Mysterious Chest it’s probably a good idea to unequip your Pet until after you open the Chest and pick up the loot.
The transmog I was looking for was The Clipper. I realized that after 20/30 runs (with the elite present), I still hadn’t gotten it, (normally I get it in fewer tries), and I decided to remove the pet. And I got it (In 2 or 3 tries with the elite present).
Bad RNG or pet, hard to know 
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In my experience, if the transmog item drops by itself, the pet will ignore it; if there is another item for the pet to pick up, the transmog item will be vacuumed up and salvaged.