There can be a number of reasons for this.
Some students have very well defined goals that cut across departmental boundaries.
This is not surprising, since the field of engineering is changing rapidly, and many areas are no longer within the purview of a single department. Consider, for example, the many intersections of engineering and medicine. Other students want to interweave elements of engineering with other disciplines not traditionally included in engineering. Still others desire to study engineering, but gain a broader undergraduate education at Stanford than the traditional engineering paths allow. Some seek unusual depth or breadth in their engineering programs.