It was a disgraceful dereliction of duty by the implementers of Aegis to recycle contact IDs so eagerly. With 4 digits it should have taken 10,000 subsequent contacts before that number came around again.
It was a lack of imagination. They didn't anticipate that case and probably just selected the contact IDs randomly. A bad RNG and an unlucky day is all it takes.
No amount of training is likely to completely remove human factors. It helps, sometimes a lot, but there's always going to be a bit of a difference thinking actual ordinance is currently headed directly at you.
They probably had second thoughts, but they got confirmation that contact 4474 was descending rapidly.