A bit more info.
The culprit to this issue is that in the function that adds the viewport and overview elements the code uses the wrapInner method.

addScrollBarComponents: function () {
this.assignViewPort();
if (this.$viewPort.length == 0) {
this.$element.wrapInner("<div class="viewport" />");
this.assignViewPort();
this.viewPortAdded = true;
}
this.assignOverview();
if (this.$overview.length == 0) {
this.$viewPort.wrapInner("<div class="overview" />");
this.assignOverview();
this.overviewAdded = true;
}
this.addScrollBar("vertical", "prepend");
this.addScrollBar("horizontal", "append");
},

The unwrap function would work if we used wrap instead of wrapInner. Although I like the idea of it putting the elements inside instead of outside.

here is a possible way to resolve the issue.

removeScrollbarComponents: function () {
this.removeScrollbar("vertical");
this.removeScrollbar("horizontal");
if (this.overviewAdded)
this.$overview.replaceWith(this.$overview.contents());
if (this.viewPortAdded)
this.$viewPort.replaceWith(this.$viewPort.contents());
},

I was having the same problem, Jevedor's suggestion worked for me.

Thanks, Jevedor's solution solved my problem!

Yes Jevedor's solution working good +1