While in dual form, if you go through a blue plant warp, Li will appear beside you on the other side. When you get out of dual form, then it is okay and you have a single Li following you. It happened to me by going through the "last" plant warp before the last boss. It may be just a little bug, but it is likely that people will go through this warp in dual form when they don't know what is on the other side, wanting to be prepared for anything.
