Here's a list of the issues that I've encountered. I sincerely hope that it helps to improve the engine.
Sound. There is often random pops when there should be silence. Parts of sounds will sometimes repeat. Some sounds are distorted, either seeming to play at a reduced quality, stuttering, or even pitch shifted.
Saving. My settings don't load correctly. I had set the control and display settings to my preference, saved them to the VMU, and reset the game. Brightness seemed to be the only setting that was set correctly, though this only took affect upon loading the next level. I haven't tried saving my progress.
Clipping. It's now quite rare, but weapons can still clip through geometry. Entities can clip through the player's weapons and HUD. The plane object used to colour the screen will clip through the geometry.
Warping Skies. The sky layer warps when the player is moving.
Menu. At its default size, the dark background of the menu doesn't cover the entire screen, with a gap down the left hand side. There is clipping on some of the scroll bars. Text looks fine at all sizes, but menu images would benefit from set scaling so that their pixels remain square. Some elements don't show as off or on when altered (such as the crosshair, which still reads as "off" when on).
Crosshair. The position of the crosshair is altered by the screen size, with it only being in the correct position when the view window is fullscreen.
Mouse Binding. The mouse is useable, but its buttons cannot be reassigned in the options menu.
Culled Polygons. The chaingun in ATF is rendered incorrectly in the latest version of 1.2, but appears correctly in the original build.
Here's videos of some of the issues. Some of the videos were made with the earlier build of 1.2, but all of the issues have been confirmed as existing in the latest build.
Sound popping :
http://pipnayler.com/misc/sound-pop.mp4
Stuck sound :
http://pipnayler.com/misc/sound-stuck.mp4
Clipping the screen :
http://pipnayler.com/misc/z-clip-screen.mp4
Entities clipping the vweap and HUD :
http://pipnayler.com/misc/z-clip-hud.mp4
Sky warping :
http://pipnayler.com/misc/sky-warp.mp4
Clipping and distorted pixels on the menu :
http://pipnayler.com/misc/menu.mp4
Incorrect positioning of the crosshair :
http://pipnayler.com/misc/crosshair.mp4
The chaingun appearing incorrectly in the latest build of 1.2 :
http://pipnayler.com/misc/vweap.mp4
Here's what can happen when there's not enough memory for textures (not an issue) :
http://pipnayler.com/misc/texture-memory.mp4
This video comes from the earlier build of nuQuake 1.2 and highlights the blurred menu images, warping sky, and bad sound :
http://pipnayler.com/misc/menu-sound-sky.mp4
