Why does the "auto set" cropping feature always seem to be off a little?

Is is picking a cropping area of a certain size to make encoding easier later or is it just bugged?

bT should no more than I, but this is my hypothesis.

Auto-cropping will always crop the movie to a perfect aspect ratio.  Meaning that if it detects the full horizontal resolution to be 680 rather than 720, a vertical resolution of 382 will automatically be assigned, but as you probably have already noticed with most movies the "screen" (viewing area) is seldom filled perfectly, and often times there is slightly more "blank space" (black bar) on the upper side of the movie than the lower (or vice~versa) and the same can be set of the blank space to the left and right of many movies.  I believe auto-cropping is merely doing some simple math, but we unfortunately find that the movie was not authored to ideal standards.

That being said, I always crop my movies myself; it's most accurate, and the time spent doing so is negligible.