I imagine that they're stylized "rips" in the denim. When you've worn jeans for a while, the cuffs at the bottom wear out and expose the threads. (or maybe she cut her jeans and turned them into shorts)
...or maybe the artist felt he needed to add something stylish and impractical. But seeing as there are holes in her shorts, the worn, torn look makes sense.
keyanf said: Pockets (Is that the first apperance of an actual pocket in Pocket Monsters?)
Yeah, they're most likely pockets. Makes sense when you look at it, and we'll finally have a suitable outfit. I've fallen for this design, it looks so... normal, like something you could actually wear and get away with.