He didn't follow the Saxo train because he was a little behind in the peloton when the split occured leaving Contador in the group ahead.
Echelons are about positioning, and while Froome's positioning wasn't good enough at that stage to keep Contador at bay, it was good enough to ensure that any group that got away would only be getting a small advantage.
Froome makes that mistake again next year, maybe he loses another minute, but the way he rode that stage in this years Tour in no way indicates that he can lose any more than that sort of margin, and in the mountains he can get twice that back on any given stage.
In the end the echelon stage probably helped froome more than it hurt him. Contador was working himself, on one of the hardest stages of the race, while Froome sat back in slipstream all day. When the Ventoux stage came 2 days later, that extra bit in the tank could have been worth more than the minute Contador gained on the flat (not to mention his team).