I'm sorry for the loss of your koi. The others are correct when they say that koi are more sensitive to water conditions than the hardier comets and shubies. Usually when fish hang out underneath a waterfall it is a sign they need more aeration, but not always. During the warmer months pond water heats up and holds less oxygen than cooler water. If you have a lot of plants in your pond, it could also be contributing to less oxygen during the night.
How big is your pond to be able to hold 50 fish if you don't mind me asking? Last time you did a water change? Have you added any new fish that wasn't quarantined? Have you added any chemicals ie; algae removers? Also, what are your water parameter readings, specifically ammonia, nitrites, nitrates, KH, GH and pH? Without knowing specifics it's only going to be a guessing game as to what "could" be wrong that caused the loss of an otherwise healthy and large koi.