We tested this where I work, and the problem seems to be specifically when you include a shortcode in a template of your block theme. Not a template part, or in the post/page content, but in a template.

It’s not great that we can’t include shortcodes in our template files, but there are ways to work around the issue for our purposes if we ever needed to, as far as I can tell. For example, we could make a new template part and include it on templates where we want breadcrumbs to show up.