Is it still green quality in game, or just when you look at it in armory or on the lists here? Most of the non-battle pets can be upgraded to rare quality, but won't show up as rare anywhere other than in-game. If you stoned it and it is still uncommon (green) in game
, even after a relog, submit a ticket. I believe that is a bug. The only one I am nearly certain can not be upgraded is the Sky Lantern
from the Timeless Isle.