Myst 4 Revelations - kept crashing with sound errors in certain places. Luckily, there was a gizmo in the inventory that allowed you to teleport to different parts of the world instead of all the tedious point-and-click to get from A to B - so I used it to avoid points where there was a known glitch.
Combat for the Atari 2600 - one of the tanks would flicker and phase in and out. It wasn't anything to do with the controller, because it worked perfectly on other games - but as kids we still played it as if it were normal.