In intellij IDEA, if a method is unused, the method is shown in a gray color. But in some cases, IDEA doesn\'t grey out the method, but when I check the references of those
Most likely it's not a bug, it's a limitation for performance reasons. Methods likely to take a long time when searching for usages are skipped.
A workaround is to run Unused Declaration inspection explicitly in all your project via Analyze | Inspect Code or Analyze | Run Inspection by Name. That'll take some time. You can also set up TeamCity server to do it for you automatically every night.