I cant see anything in the pictures but I see a possible problem in the future. IME using larger stones for substrate doesn't work well. A lot of debris, fish poop etc..... Will fall down in between the stones. It will be tough to get the debris out and it will build up and become unsightly over time. Using large rocks has the same effect as an under gravel filter IMO. All the stuff you wan out of the tank will be trapped underneath your substrate. Which we've come to learn isn't good for the tank.
As for the stuff growing. How longs the tank been up and running? As mentioned rinse your filter sponges in old aquarium water when you do a water change. All the bacteria will stay on the pad. Gravel vacuuming your tank is okay. You just don't want to be doing it every week. Maybe once a month. Some don't do it at all but if the tank is full of debris a good gravel clean will help a lot.