Chapter-wise bibliography works, but cross-referencing fails

Bug description

What I would like to do

I tried to use chapter-wise bibliographies using the Quarto extension/filter section-bibliographies, which is working.

However, when using the section-bibliographies filter, the cross-referencing fails. For example, instead of "Figure 1", there is "?@fig-mtcars--707ddefda8b9d501a1d63dad3fcb74d0cb28b51a."

What I have tried

The problem persists both in PDF (pdflatex, lualatex, xelatex) and HTML formats, and also both in individual documents and books. If citeproc: true is set, then the literature cross-referencing does not produce correct references either.

Screenshot of the bug

Steps to reproduce

---
title: "Sectionwise bibliography works, cross-referencing fails"
bibliography: references.bib 

filters:
  - section-bibliographies
reference-section-title: References
citeproc: false

format:  pdf 
--- 


# Part1

Lorem ipsum.
Read @knuth84.
See @fig-mtcars.

```{r}
#| label: fig-mtcars
#| fig-cap: Some caption
data(mtcars)
plot(mtcars)
```


# Part2

Also read @knuth84.

Here's the content of references.bib:

@article{knuth84,
  author = {Knuth, Donald E.},
  title = {Literate Programming},
  year = {1984},
  issue_date = {May 1984},
  publisher = {Oxford University Press, Inc.},
  address = {USA},
  volume = {27},
  number = {2},
  issn = {0010-4620},
  url = {https://doi.org/10.1093/comjnl/27.2.97},
  doi = {10.1093/comjnl/27.2.97},
  journal = {Comput. J.},
  month = may,
  pages = {97–111},
  numpages = {15}
}

Expected behavior

I would like to have a bibliography for each chapter without missing cross-referencing figures etc.

Actual behavior

When using the filter section-bibliographies, the cross-referencing breaks.

Your environment

• RStudio: 2023.06.0
• OS: MacOS Sonoma 14.6.1

Quarto check output

Quarto 1.6.8
[✓] Checking versions of quarto binary dependencies...
Pandoc version 3.2.0: OK
Dart Sass version 1.70.0: OK
Deno version 1.41.0: OK
Typst version 0.11.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
Version: 1.6.8
Path: /Applications/quarto/bin

[✓] Checking tools....................OK
TinyTeX: v2024.07.03
Chromium: 869685

[✓] Checking LaTeX....................OK
Using: TinyTex
Path: /Users/sebastiansaueruser/Library/TinyTeX/bin/universal-darwin
Version: 2024

[✓] Checking basic markdown render....OK

[✓] Checking Python 3 installation....OK
Version: 3.11.5
Path: /usr/local/bin/python3
Jupyter: 5.4.0
Kernels: python3

[✓] Checking Jupyter engine render....OK

[✓] Checking R installation...........OK
Version: 4.2.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Users/sebastiansaueruser/Rlibs
- /Library/Frameworks/R.framework/Versions/4.2/Resources/library
knitr: 1.48
rmarkdown: 2.28

[✓] Checking Knitr engine render......OK

Start by reproducing the minimal document in the issue with the section-bibliographies filter, then compare PDF and HTML output with citeproc enabled and disabled. Done means chapter-wise bibliographies still work while figure and literature cross-references resolve correctly.