Not quite what you want, but somewhat similar, and you might found something in the sense of what you want. In this page the author described some traits of a few creatures and briefly explained why they're irreducible grotesque; they're grotesque in a way that they couldn't evolve by a gradual accumulation of grotesqueness, they must be carefully, sadistically, planned. Too grotesque to be merely random.
http://winace.andkon.com/designed_organisms/Anyway, I can remember of some examples of simple stupidity in design. There's a beetle species whose elytra are fused, making the underneath well formed wings completely useless. Something similar happens to eyes of cryptic species of salamanders, fishes (in the genera Astyanax and some catfish species) and moles. They all have the perfect design of a camera with functional lens, muscles to adjust the focus and all that stuff, but useless, underneath fused eyelids. They are used in a minor function in some species, to give some light sense, regulating the circadian circle. As Chris Colby pointed in "the case for common descent", that's like using a complex, expensive keyboard as a hammer.
Ah, some cnidarians also have complex eyes that form images (altoght they're extremely hypermetropics), but they lack a brain to actually see something. This complex structure is again only a light detection device.
The other one I can remember now is shown in this site, the teeth of babirusa pigs, which erupt from the outer part of the snout, and as it grows it can blind the animal or severely hurt in some other way, as the curvy teeth turns against the skull.
Again with teeth, there are also snakes whose poisoning teeth are located far back in the jaws making it very uneffective to inject poison in its prey....
And our own wisdom teeth aren't so wise as a project, after all.