Same note, two voices, different duration. Notes are backwards.
If you have a note in voice 1 of, say, a minim, and the same note, say a quaver, in voice 2, voice 1 should come first in the stave followed by voice 2. At the moment voice 2 comes first, and this messes things up.
How it should look:
The workaround that you would expect to fix it (swap the voices and flip the stems) doesn't. Instead if you swap the voices then voice 1 suddenly comes first.
This seems to suggest that it's not working on the voice order, instead it's working on some property of the notes themselves to say "This one should come first", when it's completely wrong.
There is no option to override the internal decision when it's incorrect like this, and I can find on way of moving a whole note sideways, only each individual component separately, and that makes a complete mess of the whole note structure.