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There are several areas in which cryptographic vulnerabilities can be introduced.

Length extension attacks are inherent to hash functions using Merkle–Damgård.

Heartbleed was a vulnerability caused by the specific implementation of a protocol.

Using weak ciphers such as DES is a configuration issue.

Is there a formal taxonomy for issues such as this, to make communicating issues easier?

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    $\begingroup$ I would't call it formal, but CWE is established, extensive, and fairly widely used. $\endgroup$ Feb 1, 2018 at 21:10

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