When Lone Star and the princess are arguing in the desert about the luggage, you'll notice that there is a long stream of cloud in the sky clearly indicating that a jet had recently passed over prior to filming.
It doesn't necessarily mean that the stream of clouds was a jet. The "clouds" you refer to are called contrails, and they are formed when the cold air in the upper atmosphere and the moisture and ice crystals get disrupted by a fast moving object. so the clouds may have been formed by another spacecraft exiting or entering the planet's atmosphere, or even by their own crash landing. In any case, I think it still could've been noticed and edited from the final product.