note mis-alignment on piano score

Not sure there is much to be done. You'll notice that in cases where stem direction is the same between staves, the notes line up.

Hmm... Was that file imported from somewhere?
To fix:
Right click on an empty spot in the treble clef staff and open 'Staff/Part properties'.
Next, open 'Advanced style properties' and click on 'Reset to template' (at the bottom).

Do the same as above with the bass clef staff.
Result:
result scale exercise.mscz

If you wish to make staff size larger use Format > Page settings and increase 'Staff space' to 0.085in (or to 2.159mm) and produce a score size comparable to your original file.
Larger result:
larger scale exercise.mscz