The 'cargo hold count' feature in the commodities screen only recognizes identical autons. If a device or armor is changed the auton is not counted in the cargo hold.
Can lead to a "You have 2 ,,, autons in your cargo hold" screen description when you have many more autons of the same type but reconfigured with different devices/armor.
Or a count may not show if all autons of a type in your cargo hold have a different configuration.
Maybe ignore the data on the item or check the type for autons?