You're using it correctly, I believe the issue lies with pulldown_cmark_to_cmark (which is used to convert parsed Markdown back into raw Markdown text).

When I run this test:

#[test]
fn alerts_pulldown_cmark_to_cmark() {
    let source = "
> [!NOTE]  
> Highlights information that users should take into account, even when skimming.
    ";
    let events = pulldown_cmark::Parser::new(source).into_offset_iter();
    let mut roundtripped = String::new();
    pulldown_cmark_to_cmark::cmark_with_source_range(
        events.map(|(event, range)| (event, Some(range))),
        source,
        &mut roundtripped,
    )
    .unwrap();
    assert_eq!(source, roundtripped);
}

I see that the resulting Markdown has an extra line of the blockquote at the beginning:

>
> [!NOTE]  
> Highlights information that users should take into account, even when skimming.

This makes Pandoc very unhappy and it no longer considers it an alert:

• Before:

  $ echo '> [!NOTE]\n> Highlights information that users should take into account, even when skimming.' | pandoc -f commonmark+alerts -t native
  [ Div
      ( "" , [ "note" ] , [] )
      [ Div ( "" , [ "title" ] , [] ) [ Para [ Str "Note" ] ]
      , Para
          [ Str "Highlights"
          , Space
          , Str "information"
          , Space
          , Str "that"
          , Space
          , Str "users"
          , Space
          , Str "should"
          , Space
          , Str "take"
          , Space
          , Str "into"
          , Space
          , Str "account,"
          , Space
          , Str "even"
          , Space
          , Str "when"
          , Space
          , Str "skimming."
          ]
      ]
  ]

• After:

  $ echo '>\n> [!NOTE]\n> Highlights information that users should take into account, even when skimming.' | pandoc -f commonmark+alerts -t native
  [ BlockQuote
      [ Para
          [ Str "[!NOTE]"
          , SoftBreak
          , Str "Highlights"
          , Space
          , Str "information"
          , Space
          , Str "that"
          , Space
          , Str "users"
          , Space
          , Str "should"
          , Space
          , Str "take"
          , Space
          , Str "into"
          , Space
          , Str "account,"
          , Space
          , Str "even"
          , Space
          , Str "when"
          , Space
          , Str "skimming."
          ]
      ]
  ]

I'll take a look into pulldown_cmark_to_cmark and see if there's an easy way to fix this.

• This still happens on the latest version:

  Compiling pulldown-cmark v0.12.1
  Compiling pulldown-cmark-to-cmark v17.0.0
  

Unfortunately I think this'll be blocked for a while.

Newer (breaking) versions of pulldown_cmark support alerts, but I'm holding off from updating until mdbook does so (which requires a breaking change) to make sure parsing is consistent (#115).

Additionally, even the latest pulldown_cmark_to_cmark needs a fix: Byron/pulldown-cmark-to-cmark#86

Thank you for taking a look :-)

#138 implements support for alerts, although note that you shouldn't set from = "commonmark+alerts" with it because mdbook-pandoc no longer sends commonmark to Pandoc, but instead Pandoc's native AST (see #137). I'll still hold off on merging until mdbook upgrades, but if you want something to use now, that branch should do the trick.