This story has been doing the rounds recently (more here). I first found reference to it in BoingBoing (here, in fact.)
Apparently – “In Millennium Challenge, you had several cases of experimentation going on at the same time you had exercises going on,” Pace explained. “For example, if what the opposition force commander wanted to do at a particular time in the experiment was going to change the experiment to the point where the data being collected was no longer going to be valid as an experiment, then he was asked not to do that.”
Of course. That explains everything.