Built in Neo encoder cuts out when motor is being spun

When spinning a Neo 550 through our code the spark max would periodically throw out encoder errors both when spinning both manually (with our hand) and with a controller through code. After going through some troubleshooting we determined it had to be the neo swapped out that motor and haven’t had any problems since. Today we were tuning PID on the shooter and it started throwing the same errors. Unfortunately this neo is not so easy to replace. Any idea what could be causing this or any trouble shooting ideas? So far we have ruled out the encoder cable, spark max, and power going to the motor/controller.