The obvious answer is 'missing key milestones', but that depends on a structured project plan with clear milestones (e.g. waterfall model).
What are some of the not-so-obvious or subtle signs that the project is going awry? What's the best-case or worst-case impact on the project?
Please give one item in your answer so we can gather them together here and people can vote accordingly. You can post more than one answer if you have several to share. Real-world examples would be helpful.