We report on an inconsistency in the latitudinal distribution of aviation emissions between the data products of phases 5 and 6 of the Coupled Model Intercomparison Project (CMIP). Emissions in the CMIP6 data occur at higher latitudes than in the CMIP5 data for all scenarios, years, and emitted species. A comparative simulation with the chemistry-climate model ECHAM/MESSy Atmospheric Chemistry (EMAC) reveals that the difference in nitrogen oxide emission distribution leads to reduced overall ozone changes due to aviation in the CMIP6 scenarios because in those scenarios the distribution of emissions is partly shifted towards the chemically less active higher latitudes. The radiative forcing associated with aviation ozone is 7.6% higher, and the decrease in methane lifetime is 5.7% larger for the year 2015 when using the CMIP5 latitudinal distribution of emissions compared to when using the CMIP6 distribution. We do not find a statistically significant difference in the radiative forcing associated with aviation aerosol emissions. In total, future studies investigating the effects of aviation emissions on ozone and climate should consider the inconsistency reported here.