I have noticed this issue several times and tried to replicate it, in order to understand what was happening.
Upon first entering an area, creatures spawn normally at all spawn points. Once you move away far enough for them to disappear, the background engine is suppose to keep note of them and re-spawn them upon return to render distance. I can't tell if the bug is the engine not noting them properly upon de-spawn or re-spawn, but either way, they are gone.
This works on any roving ground creature (not sure about the giant giraffe things), but it does not affect the flying crab, bug plants, or gas plants. It has made collecting enough organs and carapaces difficult. I've actually gone on specific hunting trips to get them before they disappear.
I hope this helps the Dev team ID and eliminate the bug. I like having to fight the creatures, and them just disappearing takes away an important element of the game.