Hi, Carlos,
Firstly, all analog channel's allowed voltage are from GND to 3.3V, the analog channel pins ANAx or ANBx can not accept negative voltage from hardware perspective.
Secondly, I suggest you use Simultaneous mode by setting the SIMULT bit in ADC0_CTRL2.
Pls have a try, if there is still have abnormal digital sample, update the community page.
setRegBit(ADC12_CTRL2,SIMULT);//0x0000: simultaneous mode
BR
Xiangjun Rong