I found a few issues with your code, I think I've worked them out and got it working.
First fix your HTML:
<div id="container1" style="background-color:red;padding:20px">
<div class="draggableContainer">
<div class="draggable" style="background-color:blue;width:200px;height:200px;"></div>
</div>
<div class="draggableContainer">
<div class="draggable" style="background-color:yellow;width:200px;height:200px;"></div>
</div>
<div class="draggableContainer"></div>
</div>
Next You'll probably want to use the stack option:
$('.draggable').draggable({
revert: "invalid",
snap: ".draggableContainer",
stack: ".draggable"
});
$('.draggableContainer').droppable()
From the API documentation:
Stack
Controls the z-index of the set of elements that match the selector, always brings the currently dragged item to the front.