If you have a look at examples/bundlesequence.cf, you'll see an empty line right before the "#+begin_src example_output" line.
If you later look at reference/language-concepts/bundles and do a Ctrl+F for "R: Hello, main bundle.", you'll see an empty code block right before it.
Other files, like examples/ago.cf fix it by including a
line right before the "#+begin_src example_output".
Easy, but not future-proof, solution would be to add such lines to all examples.
Proper solution would be to fix our documentation generator.