Sent by Ian Hickson:
Some of the sections are empty. For example, take this markup:

   <h4 id="what-conform">2.2 What needs to conform</h4>

   <div id="implement">
     <div class="principle">
       <h4 id="implement-principle"><span class="principle-label">2.2
Requirement A:</span>
       Identify who or what will implement the specification.</h4>
     </div>
     ...

It is semantically equivalent to (removing the semantically-neutral
<div>s, <span>s, and id=""s for clarity):

   <h4>2.2 What needs to conform</h4>
   <h4>2.2 Requirement A: Identify who or what will implement the
specification.</h4>
   ...

...which means there are two sections labelled 2.2, with the first one
being empty of content. There are also examples where you have two
sections with the same number, for example there are two sections
numbered 2.3. Maybe the second set each time was supposed to be an
<h5> instead of an <h4>?