Intellij 2017.1 can't find usages after run

Recently I've had problems with Intellij suddenly marking methods and such as unused, and "find usages" returns empty results - even though I know a class or method for example is being used several places. This seems to happen after doing a run (unit tests or starting my server). The fix is to do a re-import of my maven project in IntelliJ. A couple of other guys in my workplace are also experiencing this, with different projects. Does anyone else have the same issues? Is this a bug?