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1) Spawn an ATLS (or have one handy)
2) Either have an elevator or ship with cargo containers in it
3) Use a tractor beam to begin moving the ATLS
4) Guide it into the cargo containers, and release it

What happened
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The ATLS will happily clip into the containers. In a freight elevator it will likely remain there once released, embedded inside a container. In a ship like a C2, it tends to pop out the top of a 1-SCU high container, but will also embed itself midway up a 2-SCU high stack.

What should have happened
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There should be some manner of collision between the ATLS and commodity containers in such cases.

Workaround
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Move the boxes around to retrieve the ATLS.