The only real way of retrospectively justifying that is to speculate that the aliens were waiting for sufficient red-blood-celled life to have developed for their purposes before making their move — again, this inference has the clumsy implication that they knew in advance that it would happen eventually and were waiting it out. We don't know for sure that they've been there millions of years, only that one character speculates they may have been; it could have been ten or twenty thousand, for example. The problem with this idea is that, for every human which gets "harvested", about twenty or thirty just get vapourized indiscriminately, so they can't have been that worried about it. You can conjure up retroactive explanations for this, too, but it just goes to highlight how many off-screen logical contortions must be gone through to make it add up. The other issue there is that some of the ships were buried under intersections and buildings — places which must have been surveyed fairly extensively at the time of construction. It's really got quite a few holes.