The Frank Gehry-designed Concert Hall in LA had the same problem (http://en.wikipedia.org/wiki/Walt_Disney_Concert_Hall#Reflec...). Gehry uses proprietary 3D design software based on Catia (http://en.wikipedia.org/wiki/CATIA) to design the curved surfaces of his buildings. He's spun that off as a product in its own right (http://www.gehrytechnologies.com).

In Gehry's case, they did an after-the-fact analysis and dulled some of the reflective surfaces (it's quite noticeable, going from shiny to matte). Presumably, given the trend towards more sculptural buildings, analysis of reflections will become standard. It's not hard to do.