I was having the same problem, so I checked by save folder. I had files going all the way up to slot00013, despite onl6y having one active save file. I deleted all the old saves, began a new survival game, and spawned a cyclops. It remained after I …
I've had the cyclops bug as well; only one was built and disappeared upon reloading the game. I consoled in a second one, and it disappeared on reload as well. This occurred on two separate Survival games.