That schematic is wrong. That's an older version of the schematic from before Arduino.cc and Arduino.org split, and matches the M0 PRO by Arduino.org.
If you check pins 2 and 4, you will see those are reversed as well.
Adafruit has the correct schematics here:
I guess they posted the Eagle schematic because it is easier for beginners to read than the schematic from what I assume is Altium, but they really should have updated it to be accurate.