Flipping stem of second voice -- causes it to line up incorrectly on head of note.

In Measure 41. Look at the note in the piano part -- treble clef. If I flip the stem downward it looks OK. But upward it is wrong.
Anyway, to fix this?
Thanks.
It has happened in other songs as well. I usually just flip the stem downward, but I would prefer for it to be upright and 'normal-looking'

Same thing happens in 42. First note in 41 stem is up and the same note in 42 is down stem.