When enabling "3D anaglyph mode" in Minecraft it renders the scene twice (one image for each eye) with different perspectives to get a parallax effect which helps the brain to figure out the depth in the image.
This parallax is rendered in a way that gives users headaches because the scene is popping out of the screen instead of being behind the computer screen (looking through a window). I added a screenshot to demonstrate my point about "popping out": If you look at this image with red/blue glasses you will see that the cross hair is "inside" the building but it shouldn't. Another indication that this is wrong is that the nearby objects has greater paralax (horizontal shift) than far away objects. Actually thats helping if you have spectators that don't wear anaglyph glasses but also want to be able to see "something", but it is wrong when wearing anaglyph glasses: if you look into infinity in real your eyes are looking parallel (thats telling the brain the object you are looking at is in the far distance) which means for your objects projected to the screen they should have a parallax of several inches. In Minecraft infinity has zero parallax, the status display has zero parallax as well, so they are in infinity but shouldn't.
Suggestion to fix: currently the rendering is done by simply shifting the camera for the left eye in 3D space and mix the result with the right eye image into an anaglyph image. Because shifting just the camera means that nearby objects get greater parallax than far away objects (infinity doesn't shift at all by this operation) you need to shift the result image (left eye) against the other image (right eye) by the same amount. Now: your nearby objects don't have a parallax in the anaglyph image, the eyes can focus on the screen and tell the brain they are on screen, where as far away objects has greater parallax in the image, but your your will go more parallel telling the brain that the objects are fare away.
Also see "Depth Adjustment" section of the "Anaglyph 3D" article on Wikipedia: