I'm not sure I understand what you're saying?
Do you mean that after you lifted the vehicle those lights came on or after you tried to do a ZPC?
ABS DTCs are a little weird in that there are failures that will immediately set a DTC and turn on the warning lamp (circuit open/shorted, pump failure, etc.), other failures may not set until the vehicle has been driven anywhere from 10ft or more (Zero Point Calibration issues, wheel speed sensor abnormal operation, etc.) The reason for that is because for some of those DTCs they way they are detected is by comparing how the sensors read when the vehicle is in motion vs. what it's expecting to see.
I also do believe that with the MTS system you need to follow the steps and make sure you actuate all the features towards the end of the ZPC process, otherwise it sets DTCs because it doesn't see those systems as functional (ran into that a couple times).
Also I'd just do a ZPC after the alignment for the best results in my opinion.
