Well, part of the problem was that a large part of Red's missile boats were being played by small speedboats that would have sunk under the weight of one missile, let alone the four to eight they "carried" in the exercise. Hence why blue couldn't detect them.It's not that simple. Are you aware of this :
(read carefully...)
http://en.wikipedia.org/wiki/Millennium_Challenge_2002
"An equivalent success in a real conflict would have resulted in the deaths of over 20,000 service personnel. Soon after the cruise missile offensive, another significant portion of Blue's navy was "sunk" by an armada of small Red boats, which carried out both conventional and suicide attacks that capitalized on Blue's inability to detect them as well as expected. "
ouch !