Yeah, our biology is full of kludges. Evolution doesn't lead inexorably to perfection, it leads to something that's "good enough" at which point the selection pressure to improve becomes negligible.

Classic example: the blind spot(s). If our eyes had actually been intelligently designed we wouldn't have them, instead we have quite large holes in our vision and our brains hack around this by just MAKING SHIT UP.
http://serendip.brynmawr.edu/bb/blindspot1.html

An analogy I like: imagine a cell as a house, and that it evolves a door between 2 rooms downstairs. This turns out to be useful, and there is selection pressure to have the same thing upstairs. Logically you'd think it would grow another door, in practice it's about equally likely to evolve a mechanism for moving the door between floors as needed ...