As reported on plwikipedia, the syntax highlighter ignores any markup contained within a <references> tag, specifically when this element is used to store a list of <ref>s. It is a common practice among several users to transfer all <ref> contents from the main text into a <references> (or similar) container, usually at the end of the article for clarity and organization purposes. Plwiki has long enforced the use of a {{przypisy}} template which basically hides <references> from the editor's sight while still allowing to pass a list of <ref> tags in its first parameter, in which case the syntax highlighting works nicely (example, check the "Przypisy" section). However, the plwiki community is now considering to spread the usage of raw HTML tags instead, and the highlighter has occurred to fail (example) where {{przypisy}} did not.
Related: T163238.