1. My knife disappears when using it to defend against predators then reappears a few mins later.
2. The whale creature goes to my pod and gets stuck there and flips over. If I'm inside the pod it's like an earthquake.
1. Knives have a durability so it's possible that the knife broke as you were using it. Unfortunately there is a bug that once they break, they'll show back up in your inventory later (usually on a reload) as a zero durability knife. At that point, they are invulnerable.
2. That's a known issue with the stable version, something happened to the pathing logic of most of the big fish and caused them to decide they needed to be next to your initial spawn. This was fixed in experimental so it should get fixed on the next stable update - due out soon I believe. But once you update you'll want to clear the cache to reset the creatures that are already hanging around.
Stalkers can also steal knives but as it re-appears, I'm assuming that's not what's happening (although it might be #1 bug mentioned by @TheMerricat if it also affects stolen knives).
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2. That's a known issue with the stable version, something happened to the pathing logic of most of the big fish and caused them to decide they needed to be next to your initial spawn. This was fixed in experimental so it should get fixed on the next stable update - due out soon I believe. But once you update you'll want to clear the cache to reset the creatures that are already hanging around.