There are three potential "missing" messages that you may be seeing:
Missing plugins: Some templates use third-party effects that don't come standard with After Effects.. Plugin requirements are listed on a template’s Details page.
Missing files: This message usually appears if the zip file hasn't extracted properly. For Windows users: try right-clicking the zip file and choosing "Extract All." If that option is not available, try using a different extraction program to unarchive the file. We also have a video tutorial on how to relink missing files as well.
Missing fonts: Occasionally, artists use specialized fonts in templates. (A download link is usually included with the project.) After Effects will simply change the font to one already installed on your computer.
In all cases, simply press "OK" and the project should continue opening successfully.