Describe the bug

context The issue occurs when an MD file is created and the content is set to have:

Included content directives
Numbered equations

The following MD will reproduce the issue:

# Lorem Ipsum
```{include} ./external.md

Some text followed by a numbered equation.

$$ \int \left( 2\sqrt{1+x^3} + \frac{3x^3}{\sqrt{1+x^3}} \right) dx $$ (eq001)

Another numbered equation following:

$$ \int \left( 2\sqrt{1+x^3} + \frac{3x^3}{\sqrt{1+x^3}} \right) dx $$ (eq002)

The end


**expectation**
Both equations in the file are rendered with reference numbers `(1)` and `(2)`.

**bug**
But instead the last equation gets a reference number which is missing the number, and only has the parentheses: `()`. The link actually works, but the displayed number is missing. So what gets rendered is just an open and closed parentheses.

**problem**
This is a problem because the last equation does not get a proper reference number.

### Reproduce the bug

Create a Sphinx project with this configuration:

Configuration file for the Sphinx documentation builder.

For the full list of built-in configuration values, see the documentation:

https://www.sphinx-doc.org/en/master/usage/configuration.html

from datetime import date

-- Project information -----------------------------------------------------

project = "myproj" copyright = f"{date.today().year}, My Proj" author = "Me" release = "1.0.0"

master_doc = "index" html_title = "My proj" language = "en"

-- General configuration ---------------------------------------------------

extensions = [ "myst_parser", "sphinx.ext.intersphinx", "sphinx.ext.viewcode", "sphinx.ext.autodoc", "sphinx.ext.autosummary", "sphinxemoji.sphinxemoji", "sphinxcontrib.jquery", "sphinx_disqus.disqus", "sphinx_proof", ]

templates_path = ["_templates"]

exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]

-- Options for MyST --------------------------------------------------------

myst_enable_extensions = [ "amsmath", "attrs_inline", "colon_fence", "deflist", "dollarmath", "fieldlist", "html_admonition", "html_image", "replacements", "smartquotes", "strikethrough", "substitution", ]

-- Options for HTML output -------------------------------------------------

html_theme = "sphinx_book_theme" html_title = "My project"

html_theme_options = { "repository_url": "https://github.com/mystuff", "use_repository_button": True, "use_sidenotes": True,

"announcement": "v0.19 is now out! See the Changelog for details",

}


Add a root file in the project and in the TOC add the following file:

Lorem Ipsum