I started noticing that after a cut, when homing again, the machine overruns the Y-stop and hits the metal rails, resulting in horrid sounds from the steppers and error messages on Carbide Motion. Looking at the Y-stop the red LED on the sensor and blue LED on the PCB are lit and in CM → Settings I do see the Y-stop activated.
I understand the system only uses soft-limits, but I do not see and missed steps or similar. All the cuts come out the same.
If this happens during initialization you may need to test your sensor but more likely it needs adjusting. The switches can work but not be triggered if they are too far away. So just put a metal object on the sensor and it should light up red. Then manually move your machine to the homing position and adjust your switch closer but no so close it is hit by the gantry.