A common cause of this is the unexpectedly loud sound of the natural string vibration. This can often be heard along with the alternate tuning of the string(s). One simple way to test is to use closed headphones to block out as much of the natural resonance as possible. A conclusive test is to record a sample; the natural acoustic sound of the string will not be recorded. If you continue to hear the ghost notes at the same level through the headphones, or in the recording, then there is an actual problem. Otherwise - you just need to crank the volume to overpower the acoustic sound.