Alternative [more responsible?] headline: Newly Conjectured Whale Habitat May Thwart Deep Sea Mining Prospects

I'd still read that as whales fighting 'the man', as in, they need to defend their natural home turf from destructive resource harvesting, ala Ferngully or Avatar.

They acknowledge that more research will need to be done to prove that the marks were made by whales—but if their suspicions turn out to be correct, it could impact licensing for mining in such areas.

So maybe: "Deep diving whales may cause licensing issues for prospective mining sites".

I think the issue is that the mining sites are going to cause issues for whales, which in turn causes issues for mining licensing, due to the environmental portion of regulations. The whales were there first, and your version again inverts the main topic of the article, which is actually beside the point.

If you find unexpected damage at the deep sea bottom structure, most of the time the culprit is the man via deep-trawls