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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.

Storing photos of people is a bit of a can of worms, make it even easier and just ask for ID if this error occurs.

That's true, but you'd still need to find the unauthorized passenger already on board. Without a picture you'd have to flush the plane and reboard.

Given there are thousands of security cameras in an airport, I don't think anyone would mind if one was used to record who got on the plane.

Now you are asking the right question