In Is Anybody Out There?, X.A.N.A. bugged the Superscan so the Lyoko Warriors couldn't localize the activated tower.
In Sabotage, X.A.N.A. possessed Michael Riley, and had him badly fry all the memory boards which dangerously 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.