Yes, this is problem, but two 200W lasers[0] separated by thousands of kilometres are able to filter out noise created by atoms or electrons easily. Moreover, 200W of energy applied to single atom will put away it from path of laser very quickly. At such powers and precision we may need to take into account flow of neutrino. It's possible that distant event created blast of neutrinos, which affected speed of light in vacuum.
[0]:https://www.ligo.caltech.edu/page/laser