How old/mature is your tank?
Yes, if you are putting water in too harshly, it will stir things up a bit and release a lot of bacteria, algae, fungus and and debris into the water column. The beneficial bacteria that lives in the substrate and bio media that processes the ammonia and nitrites aren't the only living organisms, they typically starch to surfaces, but it's also not the only bacteria in the tank. Some will stay suspended in the water column and usually, like you said, goes away....it could also crash your tank. When I started the hobby, my first 10 gallon got out of hand and I wasn't careful adding water...bam, cloudy dirty water and one time it never went away and I had to tear down the tank so I'd try to avoid it! Especially in smaller tanks less than 20-30 gallons. If your not getting cloudy water also(just debris) then don't worry too much, but still be careful.