Based on my understanding, this board is designed by 3rd party. Done some checking with board team, below is mapping relationship for these two pins.
Location Connector Pin Net MAX10 (U2) Pin
A J9.21 VCC_IO7 U2.117
B J8.34 VCC_IO1B U2.23
Both pins have same function the pin mishmash is because this board was design by 3rd party. Please continue with the compilations and report to us back if error happen regarding the mishmash pins point.
Could you also advice the serial # of the board?