with a way for the flys/gnats to get in there is a way for most any insect
you will need to find them look especially on the back sides of the leaves and use a magnifying glass some of our plagues are almost microscopic
begin a spray regiment every 3 days for 2-3 weeks with Neem oil and 2 drops of dishsoap drench the plants especially the undersides of the leaves
add 1 tablespoon of neem oil to a gallon of water ....use this to water your plants to kill emerging larvae
cover your soil with a layer of fine sand to stop the returning adult egg layers and increase the airflow in the grow room they are attracted to the moist soil
get some yellow sticky traps
keep an eye on the spotting this can also be Ph related