As far as I can tell from a similar experience to yours the one that actually causes the "enemy unit destroyed" message to appear gets the credit.
I once watched a Stuka divebomb and strafe a Large Cargo while my eel was on the way, it was fairly badly damaged but my eel hit and caused the fatal blow so I got the credit.
this is not 100% definite but it seems to work that way :hmm:
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