If the first container has an absolute child it takes away the document flow and it will always be controlled by the height of the second flex child. if you change the content of the #two to more you see it grows correctly. look here:
demo: http://codepen.io/anon/pen/NbWmdB
html:
<div class="wrapper">
<div id="one">
<div class="one-inner">
Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet.
</div>
</div>
<div id="two">
Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. amet.
</div>
</div>
css:
.wrapper {
display:flex
}
#one {
background:red;
position:relative;
flex:1;
overflow:auto
}
.one-inner {
position:absolute;
}
#two {
background:green;
flex:1;
}
hope that helps