The bug

Skin/head textures don't refresh their color when they were first loaded while 3D-anaglyph was turned on and is afterwards turned off.

How To Reproduce (skins)

1. Launch Minecraft
2. Turn on 3D-Anaglyph
3. Enter a world
4. Place a player head
5. Turn off 3D-Anaglyph
6. Your skin and the player head are discolored
7. Place a different player's head
8. Their head is colored correctly

Note that it significantly easier to verify this bug by starting with anaglyph on and turning it off than the other way around, as it is easier to see the broken skin texture in non-anaglyph mode.

How to reproduce (chat colors)

This also affects chat colors, but since those textures are finished after the game starts, a different process is needed.

1. Start the game
2. Enable anaglyph 3D, and then click "done" and then "quit" (do not close the game directly).
3. Start the game again. The game should start with anaglyph 3D enabled.
4. Enter a world.
5. Run the command /give with no parameters. This will cause a red error message to be output (as expected for anaglyph).
6. Turn off anaglyph 3D.
7. Run the command /give again. Note that the color is still displayed as gray, even though it shouldn't be.

Note: If anaglyph 3D mode was not active before starting the game, red text will render as red in anaglyph 3D mode as well, which might be a different bug.