The LRS Spec defines an element called a TextBlock. A TextBlock can contain multiple paragraphs. However every textblock begins on a new line. LRS link element can only point to TextBlocks. For inline anchors, something like this
Code:
this is a part of a larger paragraph with a <a name="destination">anchor</a> embedded in it.
you'd have to start a new TextBlock at anchor, but that would mean a paragraph break. Thus you can only point to the enclosing TextBlock. Sometimes the enclosing TextBlock can have a lot of content before it, thereby making the link point to a different page. Depending on how intelligent the automated conversion software is, the link to an inline element like a footnote can sometimes be way off.
So yes, it is a problem with the book, in that by manual intervention, it's usually possible to create correct links, the problem is really caused by the limitations of the underlying LRS format.