The problem you have is caused by all the garbage code left by Word. In the case of your file test9.epub, the myriads of non-breaking spaces (" ") are causing somehow that the window (the "canvas" using a simile) is much wider than the text area (look at the bottom scroll bar in the text window of Sigil). That's the cause of the shift of the text when the cursor moves from the footnote to the target.
You can solve this particular issue deleting most of the
that you have on the line 3155 on the code view.
Anyway, working with this mess of code most probably you will find many other issues.
To get a cleaner code from Word you could use a very useful macro created by Toxaris