If I let you win today, it'll be on the basis that you ride for me tomorrow, to help me up the mountains. Or maybe we'll just pay your team to ride for us wholesale (remember CSC a few years ago, with the brown enevlope through the car window.) Or it could be that I'm in a break, and I'll just pay you to let me win.
That happens all the time even in amateur racing, albeit in a much less polished and professional manner. Even 1/2 races will have some sort of structure and organisation within their team riders, working together to get their best contender the best result.
Just as an aside the brown envelope thing was one mechanic passing his phone no to another, nothing to do with CSC working for (then) Discovery Channel. But it goes on all the time, alliances formed and broken, riders collaborating for a common goal.
It was apparently Garmin team orders to chase the break down although Wiggins later said on his Twitter site that he didn't understand the logic behind it. It's not like it would have affected the overall too much.