Warm winter problems
Let me first state that koi's immune system doesn't really kick on until the water is in the mid-upper 60F. If the water is in the 50-60 degree range, bacteria and parasites will grow and multiple but the fish's immune system will be dormant.
My first year operating the pond has not been without some mistakes. My first mistake was not treating the water with salt to at least .1%. My second mistake was not treating the water with anti-bacterial/fungal medication in the fall and winter. Not doing those two things allowed the irregularly warm winter to wake the bacteria and parasites in the pond without allowing the fish to get warm enough to fight them off. All of the fish experienced some type of irritation, but my inexperience with the problem allowed 3 of the bigger koi to become seriously infected. The worst one pictured below seemed likely to die.
As you can see, that's pretty bad. My first course of action was a massive amount of salt added over the course of a couple days. Bringing the salt level of the pond from 0% to .2% (not safe for many plants). This killed all the algae in the pond, and had some detrimental effects on the bacteria in the filter, but it helped the fish. I also treated the water with primafix for 9 days straight. Then did a 50% water change and re-added salt to .2%. I fed the fish anti-bacterial and anti-parasite treated food.
At the current time, they appear to be getting better. The fungus is no longer growing back and it seems as though the fish are regrowing scales, though it's too soon to be certain. I'll have pics of them again in a week or so to show progress. Let this be an example though, of how dangerous it is to have too warm of a winter and water that's prime for bacteria and parasitic growth. So far none of my fish have died since my girlfriend and I started the pond, and a couple warm weeks in the winter almost took 3 of the biggest.