In Sabotage, X.A.N.A. possess Michael Riley, and had him badly fry all the memory boards which greatly bugged the supercomputer, and nearly lead to it's destruction.
In Hard Luck, Odd becomes glitched with a mysterious bug, and slowly but surely it transfers to the other warriors, devirtualizing them one by one. Bugs also cause the Lyoko Warriors to freeze in place and/or effects their powers. The same goes for X.A.N.A.'s monsters, however.