It all comes down to defects in either materials or manufacturing, you have to realize that even the best manufacturing process as of today, could always be made better, there are enormously huge strides yet to be made in manufacturing of things of all types. Composites, material engineering, etc.
On the scale of manufacturing hard disk manufacturers make, somewhere along the line someone or some machine is going to miss something and a defect is going to slip by them. Quality control is no simple problem, and there's still tonnes of innovation left to be done on all levels.
Hard disks will soon be replaced to some extent by flash, and I can't wait for this to happen personally. I'm now using "flash" 3.5' drive to replace the floppy disk drive I've had forever.