Question
Today my better half exclaimed, as she gazed out the window at our pond and falls, "There's a fish in the top pond under the falls!" And indeed, there WAS. Our population of koi and comets (60+ individuals) live in the bottom pond, which is separated from the top one by about 60 feet. Two pools and cascading falls between all. The top pond is under a large falls. No way a fish is going to migrate UP the falls, and no way a fish could survive the pump impeller to get sent up to the biofilter. And no way a big fish could get through the biofilter anyway.

And the new fish is BIG -bigger than any of the comets -smaller than the koi. Had it been circulated up to the top bond as a baby or an egg, we surely would have seen it before today.

Not only that, but this fish doesn't even look like any of the others except for the shiny orange-gold color. Aside from being bigger, the scales are larger and the body shape is rounder -like a sunfish or a crappie. It did appear to be sort of beat-up, but was swimming around normally. I caught it and put it in the bottom pond with the others. (Caught it with a kitchen wire strainer taped to a broom handle -brilliant!) There is a concern here about importing an infection but I'm assuming that whatever that fish carried had already been washed to the bottom pond with the others. The water circulates constantly, 10,000 GPH, 24/7. Anyway, it joined right up with the others.

So -where did it come from? Possibly a neighbor dropped it in as a joke -but they would have had to go to a lot of trouble to go get a fish for that purpose. My pet (heh, heh) theory is that it was dropped by a flying predator, and the marks on the body come from a beak or talons. There are no bodies of water nearby that could have fed the pond under any circumstances. Possibly a racoon could have put it there -but that would be a 1/2 mile hike from the nearest water -and why would a 'coon NOT eat the fish along the way?

So, other than what I've thought of...how else could it have gotten there, and how often does this kind of thing happen?

Answer
It happens pretty often with small fish.  Predators will carry fish, even long distances.  Sometimes they accidently drop the fish (like from a large bird), or sometimes they just like to "play" with their food like raccoons.  

Since the fish is so large, it would have been likely you would have seen it before had it gotten there as an egg or fry.  Eggs are easily moved by animals moving from one pond to another or on live plants.  Since you also say you don't think it's related to your fish, then it must have come in from another pond.

You can't rule out a human having put the fish there.  Otherwise, it could be a predatory bird or mammal that moved it.  If it has injuries, that would be consistent with that.  If you can get a good photo of the fish, I can help identify the species.

I once found a little shiner in my 1800 gallon pond.  Um, I never added any shiners!  There aren't any pond nearby either.  So, someone either dumped him in there, or he came in as an egg on live plants.

I have a small section on magically appearing fish at
http://www.fishpondinfo.com/ponds/pcare2.htm#where
but it's not really complete because other animals besides birds can haul in or drop in fish.

Good luck with your magic fish!