pybind11 strives to be a general solution to binding generation, but it also has certain limitations:

• pybind11 casts away const-ness in function arguments and return values. This is in line with the Python language, which has no concept of const values. This means that some additional care is needed to avoid bugs that would be caught by the type checker in a traditional C++ program.
• The NumPy interface pybind11::array greatly simplifies accessing numerical data from C++ (and vice versa), but it's not a full-blown array class like Eigen::Array or boost.multi_array. Eigen objects are directly supported, however, with pybind11/eigen.h.

Large but useful features could be implemented in pybind11 but would lead to a significant increase in complexity. Pybind11 strives to be simple and compact. Users who require large new features are encouraged to write an extension to pybind11; see pybind11_json for an example.

These are issues that hopefully will one day be fixed, but currently are unsolved. If you know how to help with one of these issues, contributions are welcome!

• Intel 20.2 is currently having an issue with the test suite. #2573
• Debug mode Python does not support 1-5 tests in the test suite currently. #2422
• PyPy3 7.3.1 and 7.3.2 have issues with several tests on 32-bit Windows.

These are issues that are probably solvable, but have not been fixed yet. A clean, well written patch would likely be accepted to solve them.

• Type casters are not kept alive recursively. #2527 One consequence is that containers of char * are currently not supported. #2245

Combining older versions of pybind11 (< 2.6.0) with Python on exactly 3.9.0 will trigger undefined behavior that typically manifests as crashes during interpreter shutdown (but could also destroy your data. You have been warned).

This issue was fixed in Python. As a mitigation for this bug, pybind11 2.6.0 or newer includes a workaround specifically when Python 3.9.0 is detected at runtime, leaking about 50 bytes of memory when a callback function is garbage collected. For reference, the pybind11 test suite has about 2,000 such callbacks, but only 49 are garbage collected before the end-of-process. Wheels (even if built with Python 3.9.0) will correctly avoid the leak when run in Python 3.9.1, and this does not affect other 3.X versions.