I think, rather, you're romanticizing what "real" engineering looks like.
Real engineering doesn't mean that mistakes are never made or that there are never bugs. Rather, it is that systems are tested thoroughly enough, and designed with enough failsafes and redundancy, that safety concerns are mitigated.
The problem in the Boeing case was not that the software had bugs. Lots of aviation software has bugs, it's actually very common. Rather, the problem was that they did not design the system to be safe in the event a bug occurred.
How that looks exactly tends to differ depending on the system. As a common example, many aircraft systems have other systems which monitor them and emit a warning if they detect something which doesn't make sense. Though this would've required Boeing to create technical material for pilots on how to respond to this new type of warning, which would've required training updates, which would've required recertification of their plane design, the cost of which Boeing desperately wanted to avoid. Fortunately (unfortunately), FAA oversight had become very lax, so Boeing instead just downplayed the safety concerns and nobody asked any questions.