I'm working on a device that used an Arduino Nano to operate multiple motors with a cumulative current draw of over 1A. Commands are sent from a computer via USB to operate the motors. The device is powered by an external 12V supply from a wall outlet, which the Arduino is meant to be powered through by the USB. Its 5V pin is not connected to the network.
I was doing some testing with a new on-off button setup and realized that when the 12V supply is absent but the Arduino is plugged into USB, the device actually draws a little over 4V through the Vin pin and into the 12V net. I don't believe the Nano has easily modified connections to change how power is distributed across its pins, and I know that powering it through the 5V pin directly will not only lead to the same problem, but also connect the USB supply straight to 5V net directly, rather than the 12V supply line that just connects to the regulators and Arduino's Vin.
I may just be making mountains out of mole hills, and I also know that with a more custom setup instead of a prefab Arduino this ceases to be an issue, but I am curious to hear how this would be tackled by others. My initial thought was just to power the Arduino through the USB and not have it connected to the 12V or 5V lines at all, with only its GPIO connected to the other aspects of the board.