When using bookdown to render to pdf following the instructions in Write a Book with bookdown and Publish with Chapman & Hall, we have found in two projects that items that are indexed in the frontmatter are given the wrong page number - they get pointed to a page of the list of figures, but not to the preface.
So, including something like this in index.Rmd (which comes before the /mainmatter command):
Basic familiarity with version control\index{version control} and ...
Gets a page number of x - which is one of the pages of the list of figures. Has anyone else encountered this? And found a solution?