Sounds to me more like a bug in an edge case rather than trying to optimize for the wrong thing.
Or (more likely, I think) the first deadhead was planned to have the pilot take over a flight which was then cancelled after the pilot was already underway.
Also sounds like a case of not throwing enough adversarial data at the system - you can't just code coverage your code, you can't even establish KPIs, you have to establish its performance under system failure (does it freeze or gracefully shut down, does it persist to disk, what happens when the disk is yanked out of the system), etc.
Very few software shops I am aware of that do anything like this.
Or (more likely, I think) the first deadhead was planned to have the pilot take over a flight which was then cancelled after the pilot was already underway.