prevent Scroll bubbling from element to window

Sorry, as far as I'm aware it is impossible to cancel any kind of scroll event.

Both W3 and MSDN say:

Cancelable  No
Bubbles     No

I think you'll have to leave this up to browser authors to fix. Firefox (3.5 on Linux, anyway) seems to have a better behaviour for me: it only scrolls the parent if the child is already at the top/bottom end at the moment you start using the scrollwheel.

Solved (for some browsers) using a simple CSS property:
overscroll-behavior:

auto The default scroll overflow behavior occurs as normal.

contain Default scroll overflow behavior is observed inside the element this value is set on (e.g. "bounce" effects or refreshes), but no scroll chaining occurs to neighboring scrolling areas, e.g. underlying elements will not scroll.

none No scroll chaining occurs to neighboring scrolling areas, and default scroll overflow behavior is prevented.

body{
  height: 600px;
  overflow: auto;
}

section{
  width: 50%;
  height: 50%;
  overflow: auto;
  background: lightblue;
  overscroll-behavior: none; /*   <--- the trick    */
}

section::before{
  content: '';
  height: 200%;
  display: block;
}

<section>
 <input value='end' />
</section>

Simply apply that style property on the element which the scroll should be "locked-in" to and the scroll event will not bubble up to any parent element which might have a scroll as well.

Same demo as above but without the trick:

body{
  height: 600px;
  overflow: auto;
}

section{
  width: 50%;
  height: 50%;
  overflow: auto;
  background: lightblue;
}

section::before{
  content: '';
  height: 200%;
  display: block;
}

<section>
 <input value='end' />
</section>