DIAGNOSIS It's a safety warning, not necessarily an error. The thermostat has been calling for heat or cool for a set number of hours straight (usually 12+ for heat, 6+ for cool) and is alerting you that something might be wrong, like a stuck relay or a system struggling to reach the setpoint.
FIX First, check if your house is actually getting to the temperature you set. If it's freezing outside and your heat pump is running 12 hours to maintain 68°, that might be normal. You can just acknowledge and clear the alert by pressing the 'Done' button on the screen. If the temperature is way off, go to the thermostat and turn the system mode from 'Heat' or 'Cool' to 'Off'. Listen. If the furnace or outdoor unit keeps running, you have a stuck relay in your HVAC equipment itself, not the thermostat, and need an HVAC tech.
IF THAT DIDN'T WORK The alert thresholds are programmable. If you get these alerts during normal operation (like in extreme weather), you can increase the limit. Go to Menu > Preferences > Alerts > Equipment Running Too Long, and you can adjust the heat and cool runtime limits to something higher.
HEADS UP Don't just ignore this if your house isn't warming up or cooling down. A system running non-stop without reaching the setpoint can be a sign of low refrigerant, a failing component, or a massive air leak, which wastes money and can cause damage.