Increasing HVAC systems’ efficiency is an important target of the research on the building sector to improve indoor thermal conditions and increase indoor air quality (IAQ), with significant savings in thermal and electrical energy use. This work provides insight into the effect that bad operations can have on a mechanical ventilation system through the application of the Fault Impact Analysis (FIA) approach. This method is based on dynamic simulations carried out with Modelica. It compares the results between “with-” and “without-” fault scenarios to define some Key Performance Indexes (KPIs) and assess the impact of different faults on the ventilation system performance and indoor environment conditions. A typical residential apartment in northern Italy was chosen for the analysis, supplied by a mechanical ventilation system whose model was built from the datasheets provided by the manufacturer. The effect of a faulty thermostat sensor with different intensities was investigated, dealing with 9 “faulty” scenarios which were run with hourly simulations between June 1st and September 15th. The KPIs for the analysis of the results compare the faults’ effect in terms of electricity consumption, thermal comfort, and indoor humidity level. The results showed that the thermostat offset has considerable impact on electrical consumption of the AHU, leading to an almost doubled electrical energy use for high intensity fault. Humidity analysis produced important outcomes, as the presence of the thermostat offset had high influence on humidity control, leading to an overly dry or humid environment when the sensor temperature is not well adjusted.