This also happens in the bookdown package demo book. On this line is an index entry in front matter ( index.Rmd ) for GitBook: https://github.com/rstudio/bookdown/blob/6ae8900f1438a463a6e14ab8ffbe75eecb1d59a4/inst/examples/index.Rmd#L54
And then in the pdf, if you look in the index for GitBook it refers to page ix, which again is a page in the list of figures.