First issue has been reported in rstudio/bookdown#1157. See discussion there for details. In a nutshell:

• Pandoc's highlighting uses KDE XML syntax file
• the KDE XML syntax file for R language does not correctly handles the new R syntax.

Current fix in rmarkdown is for html_document_base() only as a post processing - see 99df4e7 . This fixes the issue rstudio/bookdown#1157

Proper fix should be:

• Push upstream correct support for Pandoc for later Pandoc's version.
• Use the XML definition file directly in rmarkdown for previous pandoc version that won't have the updated support, using --syntax-definition flag.