What would cause an altimeter to read lower than the actual altitude?

An altimeter measures altitude based on air pressure; it relies on the standard atmosphere model, which assumes a specific relationship between temperature, pressure, and altitude. When air temperature is warmer than standard, the air density is lower than what is assumed. This can lead to the altimeter indicating a lower altitude than what is actually present. In essence, warmer air allows for more lift, so when the altimeter, which is calibrated on standard temperature, is used in warmer air, it will read a lower altitude.

Higher humidity levels do not significantly affect air pressure readings relevant to altitude. Pressure changes at sea level may affect the altimeter setting but are independent of the atmospheric temperature conditions that directly influence the indicated altitude. Thunderstorm activity can affect local pressure, but it does not have a consistent impact on altimeter readings in the way that temperature does.