I have just tried to do the same thing with the desktop version of Joplin (mac osx), but cannot see or reproduce the problem. What is your configuration ?
What I do is this, goto the menu bar, select
-> view -> sort notes by -> custom order
Once this is done I go to the notebook where this matters to me, in the notes list I drag and drop the "subnote3" or any other note into the position I want it to be.