Uh...the reasons can vary quite wildly...so I'll stick to one scope: Why does production code suck even when it's been written by competent programmers? I would argue that in a non-trivial system, it becomes difficult to program components that reliably interact with each other. If one team changes the interface to their component, that is
not as "deterministic" from your perspective, if the production workflow doesn't have adequate automated testing and so-forth.
In other words, production code can suck because you've failed to anticipate all the non-deterministic things that may interact with your system. Or you may have poorly anticipated them...which can manifest itself in the form of bloated, overly cautious or overly permissable code that becomes too hard to reason with or debug.
But this is moving far away from the original topic of why beginning coders have such problems...sure, when they start working on production code and have to deal with the complexities of the real world, they'll have to adapt. But before they get there, they have to have faith -- at first -- then the ability to confidently reason about code, step by step, in the same way that (hopefully) they've done with math equations...I'm pretty patient when teaching most beginners...but one thing that still sets me off is when someone says, "Well, the code worked 5 minutes ago, and now it doesn't"...and instead of actually thinking through the reasons why that might be (and the reasons could be quite complex, to be honest)...they just accept that as something that just happens with programming. Or even worse, start pasting in random code that worked somewhere else...which literally makes as much sense as adding random digits to an equation to get it to "work".