From the 'sound of it' the Requirements Definition probably didn't cover the Infants Case and despite the 'checks and balance' which should have picked this up it went through Alpha Testing (the Developers own test process) and Beta (Customer testing Process) without be spotted (Not very good to say the least), Once in production and the fault reported, then depending on the design, a fix could take time, I suspect the Delay put down to the problem was a catalyst to 'a sort this now' demand and resources were thrown at the problem. Whilst this speeds the fix, there is often a price (not just financial) to pay as the change cannot be tested for possible cause/effects elsewhere in the Application/Module whatever!.
Gosh Manual Check-in with DCS reconciliation. A permanent parallel run (where manual and automated systems are run together normally prior to the sutomated system going live) - A you say TB a process that 'eats' staff resouces and the reconciliation is going to throw up anomalies almost every flight.
Life just doesn't get any easier in the world of Airport Handling does it!
DIH