The short answer is, Yes, your pond can be too clean. In fact a pond that is new or overly scrubbed will often suffer from pea soup, cloudy water. Why? Well, unlike a kitchen floor where you want sterility a pond is an ecosystem with many interlocking biomes. These pieces of the ecosystem must be in balance for your pond to have clear water.
If a pond is too aggressively power washed and flushed during a spring clean, and/or the mats are overly washed you have essentially given your pond a multspectrum antibiotic and wiped out the microorganisms that keep algae and nutrients in check.
If you have pea soup and your pond is new be patient and feed it extra bacteria. Often the pond owners instinct is to drain it, wash it again and refill. This almost never works however, because you are not actually addressing the problem which is a lack of healthy micro organisms not as many assume an over abundance of them. Give it time, bacteria and yes, love. It will clear up. Think of it as the terrible twos for your pond, it will pass.
To clear your pond faster you may also incorporate what is called a Flocculant and extra fine filter pad. This will expedite the situation. In tandem continue to feed bacteria and keep your skimmer net empty.
So, if after your spring clean if you see some green left behind we didn't miss it, we left it intentionally. Last years "scum" is actually helping to seed this years water column. If you are a researcher like I am and you would like more detail on how the nitrate cycle, bacteria and higher animals keep your pond healthy shoot me an email or ask your maintenance technician the next time you see them. Our Maintenance Crew carry articles in the van on all sorts of pond care topics and would be happy to share them with you!
Always remember, a little green on the rocks is a good thing! The real problems start when your pond is TOO CLEAN :)