I clearly remember the last time I had a similar* problem I was able to kill just one alien just as geever said, yes the UI could be clearer, but it did work for me
*My case was a little different: two captured aliens arrived at my second base, which had no containment, so I transferred them to my first base, which had just enough space for them, later while the transfer was still ongoing a new captured alien arrived a the first base, no problem so far, but when I tried to transfer antimatter from my third base to my first one, I couldn't start the transfer because the destination base containment was 'overloaded' by the ongoing transfer, solution: kill one alien in the containment to make space for the extra one being transfered