Didn't Aguirre tell them to not leave the tent behind?
I'm guessing Ennis brought it down with him.
(i'm too tired now to check the movie)
When Ennis rides into the "base camp" he finds Jack starting to dismantle it. When he asks Jack why, Jack explains that Aguirre had been by and ordered them to bring the sheep down. Presumably, once the dismantling of the base camp had been completed, both of them would have had to return to where the sheep were pastured in order to "bring 'em down". When there, I would assume they dismantled the pup rent and brought that down with them as well. I assume Aguirre supplied the tents and other equipment and wouldn't appreciate part of his property being abandoned way up on Brokeback.