It's a real concern for scientific experiments. Overall, the fuel burned at the station is insignificant compared to the rest of the world. Perhaps the bigger problem is the diesel generators that provide power for the base, those run 24/7.
There is a clean air sector for this reason, where science that relies on clean air is conducted. It's upwind from the station and aircraft overflights are prohibited. There's a similar dark sector too for light and radio, where astronomical experiments are conducted.