Virtually all rotor-based cipher machines (from 1925 onwards) have implementation flaws that lead to a substantial number of weak keys being created.
Some rotor machines have more problems with weak keys than others, as modern block and stream ciphers do.
Operators of both links were in the habit of enciphering several messages with the same machine settings, producing large numbers of depths.
One such flaw was the ability to reset the keystream to a fixed point, which led to key reuse by undisciplined machine operators.
[2] These weak and semi-weak keys are not considered "fatal flaws" of DES.
Note, however, that currently DES is no longer recommended for general use since all DES keys can be brute-forced it's been decades since the Deep Crack machine was cracking them on the order of days, and as computers tend to do, more recent solutions are vastly cheaper on that time scale.
It will also take longer to check randomly generated keys for weakness in such cases, which will tempt shortcuts in the interest of 'efficiency'.