The MathJax TeX fonts used in v3 have a limited glyph coverage, and it turns out that U+0305, the character you are using for the overlain, is not in the MathJax fonts. That means, among other things, that it doesn't have any metric information about that character, so it doesn't know how to place it properly.
One solution is to use a different overlain character, like U+00AF. Since that character is starchy by default, you may want to use stretchy="false", as in
<mo stretchy="false">¯</mo>
</mover>
</math>
The fonts used by MathJax v4 (now in beta release) have a wider coverage, and include U+0305, so another alternative is to switch to v4, if you are in control over the page that you are using and its MathJax version.
Davide