Hi vinnie,
It’s an issue with version 3.9 of Python (when using pyGPlates). As you noted the seg fault happens on exiting. I’m currently looking into it and will let you know when it’s fixed (it looks to be a reference count issue in a boost-python object somewhere).
In regard to the warning messages you mentioned, there’s more recent source code (revision 33) mentioned in this post but it won’t fix the above seg fault.