A change in Python 3.9.0 introduces undefined behavior in combination with pybind11 (rarely occurring crashes, but could be arbitrarily bad). We will work around it in an upcoming version of pybind11, and Python will separately also fix this problem in 3.9.1 slated for release in December.
Details available here: https://pybind11.readthedocs.io/en/latest and https://github.com/python/cpython/pull/22670.