You could drag your application folder to the “Privacy” tab and a few moments later remove it, that ought to cause a reindexing. Maybe unchecking it and re-checking “Applications” also does the same, but I’m not sure about the later.
If any attempt to do that fails, you might want to create a fresh index following these instructions. That usually clears any spotlight problems.
Also, running so low in disk space is never a good idea, try to make some room for the sake of your OS stability. That is also the reason why restarting fixes it, because when you restart, temp stuff gets deleted and there’s more “room” to play with in your HDD. As you start using your drive, the free space is less, and services start to fail.