Question marks instead of numbers

You compile, and where a figure or equation number should be, the PDF shows ??. This is not an error in your source. It is how LaTeX renders a reference it cannot resolve yet, and the fix is usually nothing more than compiling again.

Why one pass is not enough

LaTeX reads your document top to bottom in a single pass. When it meets a \label, it writes the current number to the .aux file; when it meets a \ref, it looks the number up from the .aux file written by the previous run. On a fresh compile there is no previous run, so every reference prints as ??. The second pass reads the completed .aux file and fills the numbers in. Oleafly’s bundled compiler reruns passes automatically until the numbers settle, but if you drive pdflatex by hand, the second compile is your job.

When ?? survives a second pass

If the question marks persist, work through three checks. First, compare the spelling in \ref against the \label character by character; labels are case-sensitive and a stray space counts. Second, check where the label sits. \label records the value of the most recently stepped counter, and in a float it is \caption that steps the counter, so the label must come after the caption:

\begin{figure}
  \centering
  \includegraphics[width=0.7\textwidth]{plot.pdf}
  \caption{Convergence of the estimator.}
  \label{fig:convergence}
\end{figure}

Figure~\ref{fig:convergence} shows the effect.

A label placed before the caption compiles without complaint but picks up the wrong counter, usually the current section, so the reference prints a plausible but wrong number rather than ??. That variant is worse because it is easy to miss. Third, if the .aux file was deleted mid-run or a compile was interrupted, the recorded labels may be incomplete; recompile from a clean state.

Reading the warnings

The log tells you which case you are in. “There were undefined references” means at least one \ref found nothing. “Label(s) may have changed. Rerun to get cross-references right” means another pass will fix it. “Label multiply defined” means two \label commands share one name, and LaTeX silently uses one of them, so rename until every label is unique. A naming convention with eq:, fig:, and tab: prefixes makes collisions rare and the source easier to search; the label workflow itself is covered in numbers and pointers for equations.