I imagine the same thing happened for me at Oxford - I had a perfect gpa, top 5% GRE scores, and no lack of publishing credits, conference presentations, writing awards, internships blah, blah, blah to support my app. I cannot be absolutely certain, but the 'fit factor' was the only thing I could think of that would have held me back.
Interestingly enough, I later received a personal letter from UToronto saying exactly that -- they loved me, but my research didn't fit. =(
I was tempted to write back and say, "Fuck my plans! I'll study whatever you want!" Alas, pride forbade.