We previously saw when a Shapeshifter imitated Dean in "Skin" (S01, Ep06), that they can also imitate the clothes of the person, but in this episode the shifter takes the time to undress its victims suggesting it dons their clothing.
Except it didn't imitate clothes in "Skin" - the fact that it stole one of its target's clothes ahead of time was a plot point. There may be some confusion over the fact that it didn't steal Dean's clothes when it shifted into him. However, it did take his jacket, the most recognisable part of his wardrobe, suggesting that it had some jeans and a t-shirt already lying around from a previous victim and found it easier to just put those on instead of stripping him. None of the shifters seem capable of creating clothing. This episode's shifter might be a slightly more powerful one, or simply shifts more often because it's desperately trying to avoid death by Winchesters, whereas the last one had the situation more fully under control.