The Federal District Court in Tyler, Texas found Apple infringed on 3 patents held by patent licensing firm Smartflash, L.L.C. Apple uses the patents in question for digital management and data storage in iTunes. Smartflash has a similar patent infringement suit against Samsung and has previously sued Amazon and Google for infringement.
The controversy with companies like Smartflash, sometimes called patent trolls, is that they hold patents and license them but do not make products.
For more information on the Smartflash and Apple patent infringement suit, see this article on cnet: