Yeah if the top of the substrate is 90 underneath would be much higher.
If checking temp when spraying or changing the substrate out you can get a spike in temp because you are changing/removing basically the insulation so it will activate the thermostat to increase temp.
The probe should be at the bottom of the substrate and the snake can dig down into it if it wants more heat. But that shouldn't make it possible for the top of the substrate to be higher then the bottom, like you said happened so that's weird.