An HVAC controller may be programmed to identify one or more faults with respect to the operation of a connected HVAC system. In some cases, the HVAC controller may record a fault to a fault log and/or display an alert on the display of the HVAC controller only after a predetermined number of faults of the same fault type have been identified by the HVAC controller, sometime within a predetermined number of cycles of the HVAC system or within a predetermined amount of time.