I dislike it when running material is not legible from far away; I like to know what my fellow train passengers are reading.

Are there anymore design/navigation annoyances?

For starters, and in no particular order:

Bad/non-existent indexes/references/bibliographies

Inconsistent running heads

Bleeds that cover page numbers

Pull quotes more than a page away from their inclusion in text/don't exist in text/too narrow/too wide/poor font/style choice

Poor/inconsistent editing/spelling/punctuation/use and definition of acronyms

Unreadable/inappropriate figures/tables/other graphic material

Call-outs more than a page away/non-existing/wrongly labelled

Inappropriate/inconsistent layouts and/or spacing and/or head designations

I'm sure there's more.... :-(

The designer 'not thinking' is the major design annoyance. All these 'rules' change anyway from context to context, so forget about them. Instead make up a barely sufficient system, a system which is barely there, yet sufficient for the object.

The designer ‘not thinking’ is the major design annoyance.

Sure, but that's like saying that politicians are the major reason that our governments are useless. (And let's not go down that road, please. We all have grumpiness with our respective leaders/losers.)

Trying to come with any kind of minimal system is going to land you in big trouble, because there's just too much leeway in implementation and interpretation.

OT: There was a long stretch where my nickname in the design world was "Dirty Harry" -- if you recall from the original movie, when he was asked why he was called that, the answer was "every dirty ******* job that comes along": I lost count on how many projects I had to "save".... :-(

Part of design is the aesthetic of it all, then the other part is functionality. Especially when working with publication design.

For example.

In "Meggs' History of Graphic Design" they take a very untraditional approach to their handle of the copy. It is very "creative" but there are several things I find wrong with it.

1. The use of san-serif fonts for the body copy. This strains my eyes when all the letter forms are made up of the same stroke weight and I don't have serifs that take that guesswork out of which letterform is which.

2. The columns run to close to the gutter, so to read the copy closest to the spine I have to flatten the pages out as far as they will go, reading the first chapter was almost impossible.

3. There is no thumb-space. I can't hold the book and read it. The book MUST be set down.

When this book was designed the functionality and the idea that somebody will actually sit down and read this book was completely ignored. Granted it LOOKS nice, but reading it is a chore.

So in short, my design annoyance is neglect of the end user, the reader.

Visual Research: An Introduction to Research Methodologies in Graphic Design (AVA Academia) by Ian Noble and Russell Bestley

Over design - on most left hand pages (not on the initial chapter page or full bleed images pages) they have the page number and the page number of the next page. Is that a waste of ink or something? I am too stupid to work out that the next page is going to be 1 more than this page?
Then some of the text refers to chapter numbers. Guess what? The actual pages of the chapters only have the titles and not 'chapter 1' etc.

The actual book is full of woolly theory and concrete examples. It is easy to read, it looks 'oversize', like someone pointed a zoom lense to the pages.
I have not actually found a really good/well designed navigation in a book.
Anyone suggest a really good navigation example?

The Chicago Manual of Style is very well organized, and an excellent example of how to do things well.