Sometimes a magazine will accept a manuscript and end up not using it. Some of these magazines will then pay you a “kill fee”, which is lower payment because they didn’t use the manuscript, but payment because while they were “holding it”, you did not submit it elsewhere.
I’ve been paid kill fees twice in my career. Both were for poems. One went on to be published in another magazine. The other one was never re-submitted.
I suppose the term is because they killed the submission before publication?