Because software is full of bugs, false assumptions, and ambiguities, people make mistakes, information doesn't transfer perfectly between airlines, and rare si

Because software is full of bugs, false assumptions, and ambiguities, people make mistakes, information doesn't transfer perfectly between airlines, and rare situations become common when you are dealing with enough people. If the gate agent can't override the system, the airline cannot operate. I've lived in a number of countries in the past 10+ years and encountered more than my fair share of edge cases when flying. On the average, the gate agent has to override something 1-2 times per year when I fly internationally.