The joints and bones don't show up on my creature, or the pre-made creatures.
The number of creatures is not decreasing, but they are slowly converging towards the exact same behaviour, so it looks like there are fewer individuals (since they are perfectly overlapping each other). I have seen this happen with certain simulation settings, so try changing the mutation rate, mutation algorithm and recombination algorithm. Are you using "Chunk" as the mutation algorithm by any chance?
The easy-to-download binary is now priced to support the developer. The source code is still available in the GitHub repository linked on the page and you can build the game for free from source, requiring a Unity build and some dependencies to do so, although I do agree that making the executable paid is a bit bothersome for most of the users. Keiwan explained this change in the game’s latest changelog