The US military/intelligence apparatus is so large it wouldn't surprise me if this is yet another case of the left hand not knowing what the right is up to. Or maybe they had a vague idea, considering they didn't even attempt to shoot them down. Going off the nonchalant response, this is probably not the first time UAVs have flown over their ships. Except this time it was unplanned, and so kicked off an investigation.
I'm getting UFO crank vibes from both authors social media. Also no mention of request for comment from any official in the reporting. Just building a narrative from a selective release of FIOA requests.