It's true that Dean is probably the weakest bet in Purgatory. Being human in a world of monsters, including ones that he personally sent here, it's not fun. And of course he hates being the reason that they have to stop, and find food, and get themselves noticed because he can't move as fast or as quietly on the best of days.

It only gets worse after that run-in with the shifters.

It was just a well-aimed kick that got him, a small injury, and definitely nothing compared to some of the other stuff he's endured, but right now it's screaming at him. Every step is torture because Dean refuses to stop for the little amount of time it would take to give it a rest and let it heal. Of course he's overcompensating for feeling like the weak one, so weak that he has to team up with a vampire, and he has endured actual torture in the past. So he won't let himself be bothered by this one bum knee, even if every mile he walks on it only makes it worse and makes that limp more difficult to hide.