This is an old one, but I don't see this specific issue listed under it so here it is. I recall the Angel Beats Blu-ray (possibly the same on the DVD too) has a major subtitle clusterfuck on the final scene of the last episode. Basically it starts playing music in the background whilst both characters are talking to each other, and the result is that it translates both the character text and the music at the bottom of the screen in the same colour, so text literally obscures half of the entire screen and becomes difficult to read because the music and the dialogue are the same colour. It just kills the enjoyment of that entire scene.
I just re-watched this on the off chance I should grab a US copy instead of my UK (what with it going out of print recently) and I have yellow subs for the character dialogue, white for one set of song subs and yellow for the other, in a yellow white yellow order. Little bit sub heavy, but didn't cause much of an issue with the scene.
Is it possible that the colour issue is actually with the US version, given they love yellow subs. I'd certainly think it should be reworded on page 1 as major subtitle issue it is not.