How can I prevent the scrollbar overlaying content in IE10?

As xec mentioned in his answer, this behavior is caused by the @-ms-viewport setting.

The good news is that you do not have to remove this setting to get the scrollbars back (in our case we rely on the @-ms-viewport setting for responsive web design).

You can use the -ms-overflow-style to define the overflow behavoir, as mentioned in this article:

http://msdn.microsoft.com/en-us/library/ie/hh771902(v=vs.85).aspx

Set the style to scrollbar to get the scrollbars back:

body {
    -ms-overflow-style: scrollbar;
}

scrollbar

Indicates the element displays a classic scrollbar-type
control when its content overflows. Unlike -ms-autohiding-scrollbar,
scrollbars on elements with the -ms-overflow-style property set to
scrollbar always appear on the screen and do not fade out when the
element is inactive. Scrollbars do not overlay content, and therefore
take up extra layout space along the edges of the element where they
appear.

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