Thesis-writing is a strange endeavour. You have one set deadline - if you're full-time, it is three years, or 1,095 days, after you start (we'll leave aside how set that deadline is, for the moment). As such, you face a different beast from undergraduate or taught post-graduate study. With those, constant deadlines enable you to keep on top of your workload, taking certain essays off your hands at regular intervals.
The thesis, on the other hand, stays with you. You and your superviser can set up deadlines for when each chapter has to be drafted, and this is an important part of maintaining a steady rhythm of writing, but, unlike other degrees, you carry on working on what is ultimately the same piece of work. You get those drafts back with feedback, and you can either continue honing that chapter, or move on to another. Either way, your one piece of work is still with you.
I write this now as I have a deadline tomorrow. I am supposed to be submitting one-third of chapter 6 and one-third of chapter 3. (These two sections are necessarily connected, although I won't bore you with the details now.) The trouble is that I spent all yesterday trying to work out a problem that threatened to undermine the entire thesis, especially how chapter 5 relates to the rest of the piece. And I couldn't just put it to one side and wait until I pick up chapter 5 again because it would affect how I was going to write these sections of 3 and 6.
This is the problem with doctoral study. Anxieties about fundamental problems can strike at any point - even three days before a deadline. And these problems might not be directly related to what you're working on at that particular moment. It might be how that section relates to another that you haven't considered yet. And you can only prepare so much for such an eventuality. Thesis-writing is such an intellectual exercise, that thoughts can strike when you least expect them. And overcoming these problems may just take time - time for your brain to process what exactly is to be done about it. Unfortunately, human brains are not always such respectors of deadlines.
Fortunately, armed only with a pad of paper, a pencil, and a brain, I worked out what was wrong, discounted what I thought was wrong but was actually ok, and re-established the boundaries of what I was actually trying to say. I lost a day's work though! It is not unusual for a major problem to strike at a time that undermines your attempts to meet a short deadline. The best way to deal with this is to be flexible about your deadlines, and try to reach an agreement with your superviser about such a situation. My superviser has always been understanding when I have needed an extension. But sometimes you just have to plough on. I haven't asked for more time in this case because I think I'm going to be ok, and it would be nice to finish these pieces before I go away for the weekend.