Pin 72 is the "RX" Led, right? In fact, looking at the Due schematic, it is wired between VCC and the driver, rather than GND and the driver, which is "backward", and will indeed invert the "on" sense (LOW = ON, HIGH = OFF.)
This is pretty common; on many micros, you can get more current through the LED this way, just because of the way the physics of the output transistors works out (although that doesn't seem to be true of the SAM3X.)
It's not so much a bug, as an alternate way of implementing LEDs.
It's probably copied from the 8u2 hardware on the Uno, so that the usb code can be somewhat common. It might have been copied there from the FTDI chip schematic. It COULD reflect the original purpose - a "serial" signal state is HIGH when it's "idle"; it has transitions to low during actual data transmission.
