Yesterday my roomate was raiding the Gate of Desolation mission and his pet got a worm as well.
It never used to be that way, did ANet change something about pets and Junundu?
From the wiki: "Unusually, during this mission, pets become wurms too. They will be under the affects of Desert Wurm but they will not use skills. They do assist in battle so it may be useful for rangers to bring pets in this mission."