In this case, reliance on computer modelling could have detected the error. Knowing the mass and volume of the sub, modelling the buoyancy is simple. Keeping the model updated and verifying that it can still float should be required for a project of this nature.
Unfortunately most commercial engineering software is probably too general to know to check whether the sub floats or not automatically. That would require reading the engineer's mind. That check would need to be at least turned on by someone, if not coded into the software itself. And my experience is that few even consider turning these checks on.
If you're writing the code yourself, then it should be easy to have all sorts of automated checks. Another HNer recommended using assertions to check that the sub floats when you want it to and sinks when you want it to: https://news.ycombinator.com/item?id=22396621
In this case, reliance on computer modelling could have detected the error. Knowing the mass and volume of the sub, modelling the buoyancy is simple. Keeping the model updated and verifying that it can still float should be required for a project of this nature.