finger overwriting in the parts
It takes ages to put fingering especially when it is both left and right hand into a score. When parts are created from the score both left and right hand fingering over-write and come down in the same place, presumably attached in some default position next to the highlighted note.
Comments
I guess what you are describing is a manifestation of the known fact that manual adjustments are not kept in parts. In theory, "most" manual adjustments don't make sense to keep because so much is different about the formatting, but fingerings are indeed a likely exception. There are others too. There has been some talk of perhaps changing this behavior in the future, or at least providing more control, but nothing definite yet. See for example #110541: Manual adjustments to various symbols not propagated to parts.