So I was doing my rear brakes. I didn't know the piston should be aligned with the alignment nubs in order to slide in. I went and cut it off. Would this cause an issue? I figured it out before I did it to the other side.

From what I understand those nubs are for the parking brake, to hold the piston in place so the screw mechanism can work holding the piston in place.

So worse case scenario is that the emergency brake don't work when I pull the e brake handle, but that shouldn't be the case because one of the other side has it. Its holding strength might be weaker.

I track the car so the brake balance is very important, I will road test it and do some heavy braking and get the infrared thermometer to get some temp readings to make sure the brakes are getting about the same amount of heat.