These are called systemic failures and they do happen. Sometimes, they accumulate. We can only speculate them. There are plane crashes with triple redundant systems failed... how the hell ALL three of the redundant systems failed? Because all of them were installed on the same part of the plane which broke off. It is not an oops situation, its much more insidious. I do not know what the hell they were doing in their maintenance or whatever. I can only speculate.
1. They had a maintenance and test but they forgot to disengage real missile system from test equipment? Once, I ran a load test against a live production website... I basically D-DOS'ed it. I was supposed to target pre-deployment url but i targetted deployment one. It took us half an hour to diagnose because initial assumption was that someone from outside is D-DOSing the site. I work for one of the biggest and most advanced computer science firm in the world. It should not have been possible by design but shit happens.
2. SOP changed but actual system was still old one or vice versa. Like new SOP for lowering the reaction time but some automated safety was not yet deployed on all missile launchers OR may be they were deployed on all the actual launchers but not the training ones? Or may be training ones were due to be updated the next day?
Now coming to self destruct. I do not know what is the mechanism of self destruct. But, remember, we were at peacetime. That means all the personnels responsible for various duties might not have been on their respective "battle-stations". It is possible that even the self destruct requires authorization or rather everything requires authorization. Missile was launched due to accident or malfunction but to engage self destruct required authorization which was not there. And personnel who could do authorization came back in 10 minutes by when the missile had already landed! It is possible that those who designed protocols never thought it is possible that a missile may be flying without all the authorizations! So why cover that situation in self destruct too? Its called unwarrented assumptions and they do happen too.
Note, none of the above is a simple "Oops"... It is more involved than that.
Last but not the least, the only REAL way a system is tested if it is in continuous use... These weapons often sit idle and not ALL of their capabilities are put in actual use (thanks God!).... How do you expect them to be issue free all the time? It is said that it takes 5 iterations to remove most of the issues in a system... These systems do not under go such kind of (ab)use. They are used in very regimented way... So when something goes awry, it may be going wrong for the first time.