The killing of the two survivors was illegal because the entire operation was illegal. From Andrew C. McCarthy at archive.ph:

An explosive Washington Post report, the subject of so much discussion the past two days, says that, in the first missile strike the Trump Defense Department carried out against operatives of a boat suspected of transporting narcotics on the high seas off Venezuela, two survivors were rendered shipwrecked. As they clung to the wreckage, the U.S. commander ordered a second strike, which killed them.
If this happened as described in the Post report, it was, at best, a war crime under federal law. I say “at best” because, as regular readers know, I believe the attacks on these suspected drug boats — without congressional authorization, under circumstances in which the boat operators pose no military threat to the United States, and given that narcotics trafficking is defined in federal law as a crime rather than as terrorist activity, much less an act of war — are lawless and therefore that the killings are not legitimate under the law or armed conflict. (See my Saturday column, with links to prior posts on this subject.)
Nevertheless, even if we stipulate arguendo that the administration has a colorable claim that our forces are in an armed conflict with non-state actors (i.e., suspected members of drug cartels that the administration has dubiously designated as foreign terrorist organizations (FTOs)), the laws of war do not permit the killing of combatants who have been rendered hors de combat (out of the fighting) — including by shipwreck.
To reiterate, I don’t accept that the ship operators are enemy combatants — even if one overlooks that the administration has not proven that they are drug traffickers or members of designated FTOs. There is no armed conflict. They may be criminals (if it is proven that they are importing illegal narcotics), but they are not combatants.
Says the man who turns an eye to piles of headless cartel victims, rape trees and thousands of trafficked workers-(read slaves) -also a noted Never Trump republican.
In photos you can see the product on the boat floor.
Still the punishment does not fit the crime.
What happens when Venezuela isn’t some Falkland Islands cakewalk?