This is how Flexbox rows are expected to behave. Flexbox is not meant to recreate Masonry with pure CSS: items in one row cannot occupy space allocated for a preceding/following row (same goes for columns if you’re using column orientation). You can use align-items to prevent them from stretching, but that’s about it:
http://cssdeck.com/labs/9s9rhrhl
#container {
width: 800px;
display: flex;
flex-wrap: wrap;
align-items: flex-start;
}
.cell {
width: 300px;
flex: 1 auto;
padding: 10px;
border: 1px solid red;
}
Otherwise, you should be using the column orientation or the multi-column module (see this SO answer: https://stackoverflow.com/a/20862961/1652962)