Clearing mystery citation marks

The symptom

The document compiles, but where a citation should appear you get a bold question mark, [?], and the log contains lines like LaTeX Warning: Citation 'knuth84' undefined. Sometimes every citation is affected, sometimes only one or two. Because this is a warning rather than an error, the PDF still builds, and the marks are easy to miss until a reader points them out.

Why it happens

LaTeX does not resolve citations directly. On the first pass it records each requested key in an auxiliary file; a backend program (bibtex or biber) then looks those keys up in your .bib database and writes formatted entries; two further LaTeX passes fold the results back in. A question mark means that at the moment of the final pass, no formatted entry existed for that key. Every cause of this symptom is some way of breaking that pipeline.

Work through the causes in order

Check the key itself first. \cite{knuth84} and @article{knuth1984,...} are different strings, and the match is exact, including case. Search your .bib file for the key named in the warning; a typo on either side is the most common culprit, and the first missing-key warning in the log is the one to chase.

Next, make sure the full compile cycle ran. The sequence is LaTeX, then bibtex or biber, then LaTeX twice more. A single compile can never resolve citations, because the backend has not run yet. Oleafly drives the whole cycle automatically, but a manual build or a misconfigured editor can stop after the first pass.

Third, verify the database path. \bibliography{refs} and \addbibresource{refs.bib} resolve relative to the main file, so a database in a subfolder must be written as bib/refs or bib/refs.bib. A wrong path fails quietly, and usually takes the whole reference list down with it; see Empty bibliography for that larger failure.

Finally, match the backend to the system. A document that loads biblatex must be processed with biber. Feeding it classic bibtex produces no usable output, and every citation stays a question mark no matter how many times you recompile.

If all else fails

Stale auxiliary files can hold on to an old, broken state. Delete the .aux, .bbl, and .blg files next to your document and rebuild from scratch. The .blg file is also worth reading before you delete it: it is the backend’s own log, and it names missing databases and malformed entries explicitly.