You are correct; just turning down the volume of a track will not remove it from playback and will still draw from the polyphony pool. You must mute the track to gain polyphony.
As for the ghost note: This is probably happening because you have lowered the volume of the offending track to something below full volume. At the very end of a sequence and at the very start of the next sequence of the song, all volumes revert to full volume until an entered volume is again registered. Try inserting a volume command with the desired value at the very end of the sequence by using the step editor function and also enter the same at the beginning of the sequence just to make sure you cover both bases. I hope this helps.