It should not be surprising that a screw up like this occurred. It's common for years, or decades, to go by without the military doing something they would do a lot of in wartime. Since the end of the Vietnam war in 1972, and the 1991 Gulf War, there were no large scale movements of American combat divisions. The 1991 Gulf War didn't really give the system a workout because many of the divisions came from American forces stationed in Europe, or equipment and weapons stored in Europe. Divisions came from the United States slowly. The potential problems were not noticed. When 2003 came around, staff officers noticed. Military history is full of incidents where the major "oops!" moments happen when a war breaks out, and disaster ensues.
One of the more embarrassing (and generally unknown) problems troops encountered while being mobilized for shipment to Iraq was that there was insufficient air, rail and port facilities to move a lot of army units at once. This was particularly the case in Texas, where two army divisions were located. But it was a problem throughout the southern states, where most army divisions are based. Over the years, railroads and port facilities underwent changes that made them less useful for shipping army divisions. No one really noticed until planning was being done for moving different combinations of divisions to the Middle East. This problem became another reason for reorganizing the army to make it "brigade" based rather than "division" based. This way, brigades could be moved from different parts of the country quickly, by not overloading the transportation facilities.