But it solves the problem that if A and B both depend on C the user can pass an object from A to B that was created by C without worrying about it breaking.
In less abstract terms, let's say numpy one day changed it's internal representation of an array, so if one version of numpy read an array of a different version of numpy it would crash or worse read it but misinterpret it. Now if I have one data science library produces numpy arrays and another visualization library that takes numpy arrays, I can be confident that only one version of numpy is installed and the visualization library isn't going to misinterpret the data from the data because it is using a different version of numpy.
This stability of installed versions have allowed entire ecosystems build around core dependencies in a way that would be tricky without that. I would therefore not consider it a design flaw.