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.
Example:
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.
Comments
It seems to be happening with the chords
If you want to move them use Inspector, but it seems just a workaround
MuseScore does what is correct in most cases according to the Elaine Gould's "Behind Bars", considered the modern definitive reference on such matters. The rules are based on stem direction (not voice number, which is a purely internal abstraction) and the presence of overlaps. In this case, because the upstem note goes lower than the downstem note, it is considered an overlap situation, and thus the rule "Overlapping parts / Place a down-stemmed part to the left" goes into effect.
It is true that different publishers maybe subjectively elect to use their own rules, or may alter things here and there according to their own "house" rules. You are free to do the same, if you like, via manual adjustment. To move the entire chord at once (all notes + stem etc), simply use the Chord section of the Inspector.