The biggest problem is when users of software, programmers of software, and the software code itself have 3 different incompatible theories of how it works. So

The biggest problem is when users of software, programmers of software, and the software code itself have 3 different incompatible theories of how it works. Sometimes it gets worse still: you can have different theories according to (a) scientists doing basic research into physics or human perception/cognition, (b) computer science researchers inventing publishable papers/demos, (c) product managers or others making executive product decisions about what to implement, (d) low-level programmers doing the implementation, (e) user interface designers, (f) instructors and documentation authors, (h) marketers, (h) users of the software, and finally (i) the code itself. Unless a critical proportion of the people in various stages of the process have a reasonable cross-disciplinary understanding and effective communication skills, models tend to diverge and software and its use go to shit.