Yeah, either that neck is not from that guitar or Fender fitted a bad neck that day, the pocket's too big, it should fit snuggly.
You'll have to do the best you can and stick wood into the sides. Get some wood that is near enough the thickness you want, stick it in the neck pocket where it should go, mark with a pencil and then cut to size.
That's the only way you'll get rid of the creaking, retain a good tone and sustain.
