@awitc Almost certainly this is the wiring picking up interference, poor connections on the thermocouples, or they are grounding on the heater block. See https://docs.duet3d.com/en/User_manual/Connecting_hardware/Temperature_connecting_thermocouples#wiring-the-thermocouple
Thermocouples are susceptible to inductive interference, so can pick up signals from other wires, eg heaters using PWM, or motor wires. If possible route the thermocouple wires away from these wires, especially if you are getting interference when the heater or stepper motors are on. If not, look at the wires, check they are not grounding on metal work, and all connections are good. Ideally use shielded twisted pair wiring for thermocouples.
See @dc42 's advice in these threads https://forum.duet3d.com/post/318950 and https://forum.duet3d.com/post/270256 and have a search of the forum for other similar thermocouple issues. I'll add some of this to the documentation.
If you have a very old version of the thermocouple board (pre 2018), check if it is using MAX31855 chips. These were more affected by interference, although it is possible to add capacitors to mitigate this; see https://forum.duet3d.com/post/20525 for a hint on how to do this, though the original post was on the old forum, so is lost to the mists of time...
Ian