Thanks to https://stackoverflow.com/users/1652962/cimmanon that gave me the answer.

The solution is setting a height to the vertical scrollable element. For example:

#container article {
    flex: 1 1 auto;
    overflow-y: auto;
    height: 0px;
}

The element will have height because flexbox recalculates it unless you want a min-height so you can use height: 100px; that it is exactly the same as: min-height: 100px;

#container article {
    flex: 1 1 auto;
    overflow-y: auto;
    height: 100px; /* == min-height: 100px*/
}

So the best solution if you want a min-height in the vertical scroll:

#container article {
    flex: 1 1 auto;
    overflow-y: auto;
    min-height: 100px;
}

If you just want full vertical scroll in case there is no enough space to see the article:

#container article {
    flex: 1 1 auto;
    overflow-y: auto;
    min-height: 0px;
}

The final code: http://jsfiddle.net/ch7n6/867/