I know what you mean. In the Junkyard (ep2_outland_09) there's these cars but they don't use that cluster model.
They all have separate models with the same one texture, car001b_01, which in HL2 was a blue crushed hatchback, and Ep2 replaces it with a brown hatchback, like you said. Not only that, but HL2's model had two skins, blue and red, and Ep2's doesn't, it only has one texture.
So all those cars in the game are the same brown car. Now, the cluster models, if you place and align them, match those separate groups of cars perfectly.
I think what happened is they made the cluster models for the area, assigned a separate texture for them (car001b_03, which is missing), but then went with separate cars after all.
(It's for the best because separate ones have LODs and cluster ones don't...)
And I think car001b_03 is simply that brown texture, that for some reason got saved as car001b_01, overriding the blue one. Maybe they forgot or didn't want to spend extra time adding a third skin to the hatchback model. Ep2's models have a bunch of trivial issues like missing surfaceprops (trees and stumps have it), odd mass values and stuff like that.
Either way, we ended up with three hatchback textures across two games - blue, red and brown. Only we never see all three together, because the brown replaced the blue.
So what you can do to make it not missing, is copy the materials\models\props_vehicles\car001b_01.vmt from HL2 into Ep2's materials\models\props_vehicles folder, and rename it as car001b_03.
It'll still be pointing at car001b_01.vtf, which in Ep2's case, like I said, is the brown one. But will work on the cluster models, making them identical to the Junkyard cars.