I think the problem here is the environment. In industrial control systems one input can be enough as you can control the environment. When you get to planes or cars inputs can be faulty so multiple are needed for verification.

The clock was a mission elapsed timer, which tells the system how much time since launch and what action to take.

One would expect the mission profile to consist as waypoints with the ship taking action to get to a waypoint and actions triggered when they reach one. This is generally what's happening when we talk about autonomous vehicles.

What we are hearing was it was a simple list. The problem here is the system is pretty much assuming everything has gone perfectly.

In this case they had GPS, GPS isn't great at altitude but good at providing your position. Had they simply placed a list of positions against he mission elapsed timer the system would be verifying that it's taking the correct action.

If you have sensors is best to give them a quality rating and use them to validate your system.