After looking into this more in details, this is related to Pandoc changes in 2.11.2 but it is rmarkdown related as some CSS is required.
Try this as a workaround
---
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
```{css, echo = FALSE}
div.csl-bib-body { }
div.csl-entry {
clear: both;
$if(csl-entry-spacing)$
margin-bottom: $csl-entry-spacing$;
$endif$
}
.hanging div.csl-entry {
margin-left:2em;
text-indent:-2em;
}
div.csl-left-margin {
min-width:2em;
float:left;
}
div.csl-right-inline {
margin-left:2em;
padding-left:1em;
}
div.csl-indent {
margin-left: 2em;
}
```
```{r setup, include=FALSE}
knitr::write_bib("knitr", "packages.bib")
```
See [@R-knitr]
# References
I'll open an issue in Rmarkdown. Thanks a lot for the report about this !