Well, I've learned programming (several other ghere have, too), and I must say that at some point there are so many modules working, bound together, that simply the overview is getting lost.
Unless everything is very strict and "clean" programmed, and you have good plans how all the modules interfere with one another (or rather should interfere), the overview is simply lost and you can't predict things, because there are simply too many of them.
Look into a hive. Can you say what each individual entity in this hive does ? And how it contributes or interferes with the whole ?