This happened to me also but the steps to recreate were:

Inventory full
Fish on ground
Use kitchen knife to prepare fish
No filets on ground as as expected

I did it twice, once near water edge and the other well away.

I confirm, in 0.48 stable, but this is in fact happening when you don't have the free slots into your inventory, fish filets appear correctly (x2) only if free empty slots are available, if not, filets destruct or appears under ground level who knows ...

I also found another bug and tested that out in 0.55 stable. If you have the fish in your inventory and pull the knife to the fish and click "prepare fish" you will only get the guts out of that in your inventory.

BUT, if you lay down the fish in front of you and equip your knife, and use "skin and quarter the body" than u will get the filets and the guts in your inventory.

I dont think the devs created the option "prepare fish" if the fish is in your inventory for just getting guts out of that. That makes no sense am I right?

Geez if you or other devs read this, please read my note above and test it the same way. I know u closed reports with the same issue, because u cant reproduce the bug. But in all these reports there was never explained exactly how they have reproduced this issue.