This is far from the first time that we've seen this kind of problem crop up. Google has become rather big, and it is very compartmentalized. Each group within Google can be so focused on their goal that they are unaware of the bigger picture.
I consider it a major "growing pain" of the kind that afflicts many organizations. I see it with my larger clients quite frequently - IT makes a move that makes sense, but just within their viewpoint. In actuality, they end up zapping the in-house SEO efforts, or the marketing department goals.
Google is still immature as companies go, a youngster whose growth spurt was rather astounding. The webmaster community will (and should) call them on their worst "adolescent" missteps. Our viewpoint is external and we will notice some things before anyone within the plex does.
As another side note, at the Austin Pubcon, Matt also mentioned that the Google Analytics team also hit the roof about this particular problem.