I'm just curious if this is a known issue or not. I shot the cockatrice out of the sky which also ended up dealing a killing blow. It came down in a nearby river with nothing to activate while swimming to get the trophy.

Look around for land where it died, normally it would drop there, even if it's 10 feet away. Otherwise check underwater?
On the minimap it should show a red dot with an X on it, that's where your trophy is.

No, I've had this problem too. If you knock a flying monster out of the air over water with the bow it ends up in the water but you can't interact with it. No loot, no trophies, nothing. When it happened to me (twice, second time was to prove it to myself) it lay in the water making really sad noises, but just didn't die. No health bars, but also no interaction, and no marker for the corpse.

You're talking about the Shrieker contrac, right?
I've finished that quest and didn't get the achievement either but I have the achievement for completing all the contracts in the game.

You only get loot from things you kill on land or in very very shallow water, like foot deep or marsh/swamp. Make sure you kill things you want loot from while they're on land, keeping distance from the water. If it's a trophy kill, then definitely be careful to stay away from the water.

Just reload the save game you made from 2 seconds before the fight started and re-kill it on land and you're good to go. That's what I do when dumb shit like that happens. :) Of course I'm a manual savegame whore so I _always_ have a savegame to go back to which is seconds to minutes old max and replay to correct problems and I do not use quicksave which saves overtop of itself.

I kept all of the trophies I got since the beginning of the game for a while because well, they're trophies afterall right? But eventually the weight of them adds up and takes a large chunk of your encumbrance amount away for storing shit in your inventory. Eventually I decided that I was going to have to sell off excess trophies and just keep one of each bonus type, selling extras. That minimizes weigh-down from them and allows me to carry more crap before becoming overburdened.

It'd be nice if Geralt could mount them on a wall at Kaer Morhen in his room or something.

One exception to this I have seen is when you kill thing from your boat. I've had the corpses floating on the water but their lootable fragments on the bottom of the sea directly below their corpses.. but this is not the case with the OP.