Which rmd format are you using ? html_document ?
Can you share a reproducible example ?
This works for me by inserting the citation in footnote too
---
title: 'citation in footnote'
output: html_document
bibliography: packages.bib
---
```{r, include=FALSE}
knitr::write_bib("knitr", file = "packages.bib")
```
See [@R-knitr]
We try something with citation in footnote^[Here is the citation. See [@R-knitr]]
# References
