LaTeX.org

If figured out what causes the problem: it's the addition of the option "sort&compress" for the natbib package (\usepackage[sort&compress,comma, numbers]{natbib}). It makes multiple refs [1,2,3] appear as [1-3]. Since 2 isn't on the page, it doesn't get backrefs. 1 and 3 are fine (page(s) still ...