They take issue with a "media system and method of progressive musical instruction" being used in Rocksmith, because they claim it's patent technology, which was filed October 2010.
Ubisoft's Rocksmith launched October 18th, 2011 in North America and is due in Europe this September. Ubi claim it took inspiration from Game Tank's Guitar Rising.
Guitar Apprentice's patent describes itself as: "A method is provided for progressive musical instruction using a media system with processor-executable software modules storing musical performances each having a plurality of segments." UK band Rocksmith is already in legal proceedings with Ubisoft over their trademarked name.
This is what happens when you get corporate suits in your Rock'n'Roll.