When I click on a reference in the online Q-Chem manual (https://manual.q-chem.com/5.3/bib.html), it takes me to a list of references that are not numbered, and does not indicate which reference I clicked. Not sure if that’s just a Safari issue or also the case on other browsers. Maybe it would be better to number the references in the online references page?
This happens because the bibliography in the HTML manual is alphabetical by author, and I don’t like it either. It means that refs appear out of numerical order in the text, so where multiple papers are cited at once there is no connection between the numbers, and furthermore these refs are then not grouped together in the bibliography. It may have to do with how the LaTeX manual is converted to HTML. I suggest that you make a suggestion on Trac for a “feature request”.