It looks like a bug where box-sizing is not being taken into account when calculating the size using the flex property. As the border takes up 2px, it is larger than 50% and thus only one fits on a line, so all boxes are stretched to the full width. You can see the same thing happening if you disable the border and add 2px padding instead.
You can make it work correctly while keeping the borders by adding max-width: 50% to the .box ruleset. Otherwise you can use a flex value between 33.34% and 49%. This will make the width less than 50% including the border, and as the elements grow to fill available space, they’ll still be 50% of the flex container. Kind of a ugly hack, but it will work unless you add a combined border and padding larger than 50% minus the flex value you set.
Perhaps a better way than decreasing the percentage value directly is to use calc(). This is supported by all browsers that support the modern Flexbox syntax. You just need to subtract the combined total of the left and right paddings and margins from the percentage value you want to use. As you‘re doing this you don’t really need the box-sizing property so it can be removed. There seems to be another issue in IE where you can’t use calc in the flex shorthand but you can use it in the flex-basis property, which is the one you want.
.box {
border: 1px solid black;
/* additional styles removed for clarity */
/*
50% - (border-left-width + border-right-width +
padding-left + padding-right)
*/
-webkit-flex-basis: calc(50% - 2px);
flex-basis: calc(50% - 2px);
}
See the demo: http://jsfiddle.net/dstorey/78q8m/3/