Ah yes, fish that get stuck or disappear in holes, usually catfish. Happened to my sister once. Let me let her tell you in her own words. She posted this on a family forum:
I have a Jaguar Catfish I got when he was very small. They are from the Amazon which has dark water so they like dark places. I found two clay pipes, one a bit larger than the other, that Bill had in his box of extra fish stuff, so I put them in the aquarium for the fish to hide in. He promptly went into the smaller pipe and hid. Since he would only come out in the dark to eat, he was rarely seen, unlike the two little Blue Rams in the same tank who are all over the place. Then lately I noticed his tail poking out of the smaller pipe. Hmmm, I thought, he's getting kind of big. I told Bill that if he got much fatter, he was going to get stuck in the pipe. Well, he got fatter. He got stuck and could not get out. He tried but just managed to turn the pipe upside down with him in it. How do you get a fat fish out of a pipe? Can't grease him up. There was only one thing to do. I asked Bill for help. He got a towel (one of the best ones of course) and wet it down in the fish tank, then took out the pipe with the fish in it and rolled it in the towel. Then, as he raised the hammer (my best one of course), I heard a mewling sound from the towel. Sounded just like a kitten in trouble. It was the catfish! He thought he was going to die! Bill smacked the pipe in the towel, pulling back, the pipe cracked in two the fish flopped free and he got dumped back in the tank. He lives!
This was over a year ago and that Jaguar Catfish is still around, although last I heard one of the Rams had died (probably due to old age.)
The only way I can think of to stopper up the holes off hand is either to a:
get some more driftwood of the branch variety and carve some plugs and whack them in b:
fasten some mesh over them with stainless steel staples/nails/screws what have you (good luck finding them!) or possibly c:
(probably the easiest route) filling in the holes with spray foam. There is some foam that's supposed to be made for pond/water feature use that is a dark/black color. It's used to seal spaces between rocks when constructing waterfalls and suchlike. Don't know where to find it offhand though.