Hi,
Sorry for the late reply - I'd replied earlier but must have lost it in the shuffle of multiple windows
I've written up the issue of these particular notes not allowing a stem both for upper and lower voicing. I know that some of these are bug issues, but some (eg coincidental notes with whole notes) are aesthetic issues, and different notation "experts" differ on how those should be notated.
Sorry for the inconvenience in your transcriptions at this time.
ttfn,
Sherry