Apple Configurator is DEP aware

Since version 1.6, Apple Configurator has been DEP aware. Prior to this version, if you used Apple Configurator to update he iOS en-masse on a group of iOS devices, it would activate the devices irregardless of their DEP status. With version 1.6 and newer, if your device is in Apple's Device Enrollment Program and associated with a MDM server in your DEP portal, Apple Configurator will update the iOS but will not activate the device.

As you can see, upon initial inspection, it appears something went wrong. However, if you dig a bit deper:

It is important to note that your device needs to be in your DEP portal AND associated with a MDM server in order for Apple Configurator to not activate the device, which is what many IT administrators are going for in a zero-touch enrollment situation.