The word 'mal' means 'bad' or 'poor'. 'Malalignment' implies that the relationship or geometry of one bone in relation to its neighbouring bone is outside of what one might consider normal.
Patella malalignment, pain and patellofemoral progression: The Health ABC Study. Hunter DJ, Zhang YQ, Niu JB, Felson DT, Kwoh K, Newman A, Kritchevsky S, Harris T, Carbone L and Nevitt M. Osteoarthritis Cartilage. 2007 Oct; 15(10): 1120–1127.