For example, Python's lack of support for nested dependencies means that it can be extremely difficult to use small "utility" libraries like six as subdependencies without running into potential problems from conflicting version requirements from other dependencies.
Additionally, Python's management of different types of dependencies is very weak, specifically with regard to setup.py and requirements.txt. npm has (among other things) very nice explicit concepts of development dependencies and regular dependencies, in addition to application shrink-wraps, which gives library maintainers very easy ways to split out different kinds of dependencies, or lock down all dependencies and subdependencies, using the same set of tools.
While I can say that the current version of pip, especially in conjunction with pip-tools, is significantly better than earlier iterations of Python packaging, I strongly hold that Python packaging is substantially worse than at least one other prominent example.