One of the biggest issues writers struggle with is clarity of structure, telling a book-length story that makes sense all the way through. Just writing a straightforward narrative from a single POV in a more-or-less unbroken span of time is hard enough. The further your storytelling method gets from that, by shifting points of view, changing timelines and settings, mixing narrative styles and the like, the less clear the narrative becomes to your reader, and the more careful we writers must be to make certain our readers can follow us along. Unless, of course, your intent is to confuse or bemuse your reader, in which case you should ignore the remains of this post. But let's assume you want your narrative to be completely comprehensible to your reader, and talk about some issues that affect clarity.
First issue: The writer is unsure of his intent. I know that in my own writing, there have been passages where even I'm not able to say exactly what is going on. A scene or bit of dialogue is vague and while it seems important, nobody can point out why. This happens when I don't quite know what I want to happen. I know that I need some kind of scene there, but I don't know exactly what that scene should be, so I put in a sort of placeholder and hope it all becomes clear later on. Scenes like this are not only useless, because they add nothing to the story, they in fact do harm by baffling your reader and possibly putting them to sleep as you ask them to tread water or run in place for a while as you think about your story and then move on.
Second issue: The writer forgets that the reader is not a mindreader. This is what happens when the writer makes some sort of shift in the way the story is being told and forgets to tell the reader the shift has taken place. For example, you change POVs with each chapter or several chapters, and you don't bother to show right away that the POV has changed. The reader is suddenly in the land of "Huh? What the hell is going on?" That can be cool if you're going for that effect, but if you're not, then pay attention to the clues you give (or don't) to the reader.
Third issue: The writer puts in vague transitional devices. This is similar to the second issue, but the writer thinks she has warned the reader that the narrative has switched from, say, first-person action in the "story present" to journal entries or letters or something else. Often this is accompanied by a change in POV or voice or verb tense, but sometimes not. It can look, to a reader who hasn't been warned that he's now reading a diary instead of being told a story by a narrator, like nothing more than sloppy writing.
The second and third issues frequently crop up when we're trying to be subtle and not hit our readers over the heads with big signposts saying "POV SHIFT HERE." One thing I've learned is that what we think is subtle is often merely invisible or nonexistant to readers, and what we think is heavy-handed is often not. Because we are so familiar with the story, we sometimes lack the critical distance to know the difference. This is why trusted readers are important.
So, the big lessons here:
1. Know what you mean to say, and say it. If you have to explain it to a reader outside their reading, the words on the page don't work and have to be rewritten.
2. The more clever you are with structure, the greater your chance of losing your reader, so be prepared to do extra work clarifying what's going on. Books that shift POVs often have chapter titles with the POV character's name for this reason.
3. The more literary devices you employ, such as journals, letters, found books and the like, the more work you have to do to set those passages off from the rest of the narrative.
What's the best way to delineate between these changes in structural elements? Contrast. If your POV characters all sound the same, why are you bothering? If your narrator's journal entries sound like her narration, what's the difference or the point? Don't just hijack someone's storytelling methods because they were cool in his book; make sure they have an actual function in your own book, and think in terms of function and not of coolness value. If it doesn't make sense, it is nonsense, right?