In Emacs 24.3, comint-highlight-prompt allows ANSI colors to show through if it does not specify any colors itself. In Emacs 24.4, it does not, even if comint-highlight-prompt is the "empty face".
To reproduce, set PS1 to something containing ANSI color codes. M-x shell (and M-x ansi-color-for-comint-mode-on if necessary). Then use ls --color. In my case the color in the prompt is ignored, but the output of ls --color has the expected hues.