![arXiv doesn't run BibTeX. That's why your references show as [?].](https://media2.dev.to/dynamic/image/width=1200,height=627,fit=cover,gravity=auto,format=auto/https%3A%2F%2Fdev-to-uploads.s3.amazonaws.com%2Fuploads%2Farticles%2Fm7ei1mggwegmcm2di86v.png)
When you compile locally: pdflatex → bibtex → pdflatex → pdflatex. arXiv runs pdflatex only. It skips BibTeX entirely.
So if you upload your .bib file and expect arXiv to generate your bibliography, it won't. Every citation becomes [?]. Your paper technically "compiles" on their system but the reference list is broken.
The fix: include the pre-compiled .bbl file in your upload. You generate it locally, then include it alongside your .tex. There is an extra wrinkle if you use biblatex: the .bbl format is version-sensitive and must match arXiv's current TeX Live distribution, otherwise you get cryptic errors inside the .bbl itself.
The second most common failure is a hyperref option clash. arXiv injects its own hyperref, which conflicts with your \usepackage[options]{hyperref} call.
If your arXiv submission keeps failing, the arXiv LaTeX formatting service at The LaTeX Lab specifically handles these , .bbl generation, hyperref conflict resolution, figure format unification, and source cleanup (since arXiv makes your .tex publicly downloadable).
