I'm having the same problem with this mission. I filmed the first group of whales, flew to the second marker and filmed that group, found the cargo ship, flew to the third marker and found nothing. The marker says the whales may have moved, so I flew the northern zone until my fuel light turned red, twice. I drove off the whale about to beach itself, and reported another beached whale, but still haven't found the ones I'm supposed to film. I've noticed that you have to fly under 1000 ft or so for the objectives to trigger.