I can think of a few ideas (I fully admit, these are just guesses, although based on remembering my own experiences and experiences of people I went to school with).

First, in the general space of a **lack of motivation**:
* One of the comments in the comment thread suggested this could be a form of burnout, where the students have worked hard on the project, and are tired and do not have the motivation to write it up. I think this is plausible. 

* Another plausible, related explanation is that some students toward the end of a degree have lower motivation to focus on their studies ([senioritis](https://en.wikipedia.org/wiki/Senioritis)). 

* Students may enjoy the technical aspects of solving problems, but find the writing aspects boring and simply not *want* to do it, or not think it is really important, and therefore not put as much effort into it.

Second, in the area of a **lack of experience**:
* It's tempting to focus on major issues first and then move onto "easier" issues later, whereas at least I've found as I've gotten more experienced that it's actually better to fix the easy things first.
* A lot of work at the undergraduate and masters level is "personal", in that it only really affects the student (you are responsible for your own grade, for example). At higher levels, work is more collaborative. So, when they turn in messy work, they may only be thinking about how this affects their grade, and not thinking about how they are creating more work for you, or that this piece of work is meant to be read by someone and communicate information. I realize that might sound silly, but I think there is a mindset shift that has to occur in at least some students between "I am turning this paper in for a grade" and "I am writing this paper because I want to communicate ideas to others." 
* Students have probably never written a document of the scale of a thesis before, nor one that will be read as carefully. Perhaps they have bad habits from skating by in courses with writing assignments. (Even talented students can develop poor writing habits that "work" for some courses but eventually do not). It is always difficult to change bad habits, and now they are in a relatively high-pressure situation to produce a thesis, which can only make it more difficult to change those habits.
* In computer programming, there is an idea called [technical debt](https://en.wikipedia.org/wiki/Technical_debt). If a programmer chooses an easy and fast, but ad hoc solution, they accrue some "technical debt" that must be repaid in the sense that eventually that code should be rewritten in a logical and coherent way. Eventually, if one waits too long to pay off the debt, the code becomes a disjointed mess that is difficult to maintain and costly to convert into something more streamlined. A student (especially one who wants to minimize the amount of time because of burnout or lack of motivation) may feel that the most important thing is to produce *text*, and accrue some "writing debt" by saying that they will fix "trivial" issues like typos and references later. They don't realize that this writing debt can quickly build into a lot of work -- for them, and for you. Perhaps they even intended to fix typos, but produced a lot of text accruing a lot of writing debt, that they did not have time to pay off before the deadline.

The common themes in these scenarios (which, I admit, are just guesses) are an overall lack of motivation to deal with writing issues, a lack of planning, and a certain degree of self-absorption to not think about the effect this has on the people reading their thesis.

In terms of how to produce better behavior, as always there are "carrot" and "stick" options. The "stick" options are probably more obvious (but also likely to increase anxiety, which could be a factor, as another answerer pointed out), and include things like
* Explaining clearly that their grade will suffer if they don't fix the issues.
* Refusing to accept written material with a lot of typos and broken references.
* Confronting the student during feedback meetings to explain your disappointment in their work. "I expected more from you.",  "Do you think this is acceptable?" etc.

The "carrot" options (which probably require more work on your part to be creative and to implement, and thus might not be practical, and might also be considered unnecessary coddling by some people) might be things like
* Rewarding behavior that you want. ("I noticed this section was well written compared to the others, nice work, please apply this to the other parts of the text.")
* Offering to check in with a struggling student before their next draft is due to see if they are accruing writing debt, and offering advice on what to focus on before the next draft is due.
* Take one chapter draft and ask them to focus on the writing aspects for a given draft, even if that means they don't fully complete all the content for that chapter. You want to see a polished draft of *something*, just to force them to work through the writing steps. The idea here is that they can use this draft to build up the writing skills they may be missing that they can then apply to other sections. At least they'll get an idea of how much time it takes.

Another "off the wall" idea could be to have students read and critique chapters of each others' thesis. I took a course in grad school where everyone was a reviewer of everyone else's paper. This could create some positive peer pressure to create a good version of the draft. And, making someone give feedback on someone else's work, can make them think about what someone is looking for in their work.


It may be that some students just don't want to do the thesis, and nothing you can do will help them write a better thesis. However, as an optimist, I have to believe that if there are such students, they occur at a rate far below 10%.