By analysing a large set of St. Santin F region Incoherent Scatter (IS) data for low solar activity we find nighttime ion temperature (Ti) on average to be apparently slightly higher than electron temperature (Te). We show that this difference is a bias incurred by the IS spectral analysis procedure owing to the neglect of H+ ions in the 300–500 km altitude region. Further, we show Te and Ti to depart from the neutral temperature Tn with increasing altitude. We perform a simulation of ion and electron temperatures and show that the difference between Ti, Te and Tn can be caused by the presence of a small amount of hot oxygen. Using our simulation we estimate the ratio of hot oxygen to cold oxygen density to be 0.13% on average at 400‐km altitude for low solar activity.