Yes they definitely can and I've battled them indoors myself but I'm thinking about the real high end grows that make the chances extremely low for pest invasion. Or any indoor grow in theory that doesn't happen to have a bug problem where things like humidity, temp, watering, airflow, air quality, feeding etc. are all controlled for "optimum" growing conditions. Is it really optimum after all
Unless you are sterilizing everything entering the cleanroom, that is simply not possible. Fungal spores, bacteria, and viruses are everywhere. If one of your workers is a smoker, they can spread Tobacco Mosaic Virus, for example.
Clean rooms are not perfectly clean. I've always wondered if Intel, which is famous for wanting all of their fab cleanrooms to be the same, also infects them with the same bacteria and mites...