Quick answers to four problems that trip people up most. Each links to a fuller page.
Japanese not showing / garbled
Almost always the wrong engine or encoding. Use a Japanese setup, not plain pdflatex — uplatex (+ a js/jlreq class) → dvipdfmx, or lualatex + luatexja. Save the source as UTF-8, and make sure a Japanese font is configured (kanji-config-updmap for dvipdfmx; \setmainjfont for LuaLaTeX-ja). (See “Japanese typesetting methods” and “Encoding & newlines.”)
Fonts not embedded
Journals, PDF/A, and print require embedding. pdflatex/lualatex embed by default; check with pdffonts file.pdf (each font should read “emb”/subset). If one is not embedded, it is usually a bitmap (Type3) or a base font — switch to a proper Type1/OpenType font. For guaranteed compliance, use pdfx (PDF/A). For Japanese via dvipdfmx, set the embedded font with kanji-config-updmap. (See “PDF/A & accessibility.”)
pdffonts document.pdf # 各フォントの埋め込み状況を確認 / check which fonts are embeddedReferences stay ??
Compile again — \ref reads the previous run’s .aux, so it takes two passes (latexmk does this for you). If ?? persists, the \label is missing or misspelled; for citations, run bibtex/biber. (See “Undefined references & duplicate labels.”)
Image not appearing
Check the format matches the route — pdflatex takes PDF/PNG/JPEG (not EPS; convert with epstopdf), while the DVI route via dvipdfmx accepts EPS too. Verify the file path and extension, and \graphicspath. Also, draft mode replaces images with a box, so turn off draft for the final. (See “Producing PDF.”)