Here is a reproducible example:
---
title: "Untitled"
date: "`r Sys.Date()`"
output: html_document
bibliography: packages.bib
csl: https://www.zotero.org/styles/vancouver-brackets-only-year-no-issue
---
# A header
```{r setup, include=FALSE}
knitr::write_bib("knitr", "packages.bib")
```
See [@R-knitr]
# References
Can you share your pandoc version ?
rmarkdown::pandoc_version()
I cannot reproduce using Pandoc 2.7.3 but I can using Pandoc 2.11.2. It could be a pandoc issue.