Yes this is a mistake that will be corrected the next pass. It has no affect on the operation of the board as the SW writes over the registers on boot up…
The issue is described here http://circuitco.com/support/index.php?title=BeagleBone#Etherent_PHY_Default_Confiuration_.5BA3.2CA4.2CA5.5D
And, it is described in the Rev At SRM as well. http://circuitco.com/support/index.php?title=BeagleBone#Rev_A6
And here under changes http://circuitco.com/support/index.php?title=BeagleBone#Revision_A6
Gerald