One is that the star may naturally not be putting out the usual smooth amount of light, which seems unlikely. It could be a very rare phenomenon, but stars have behaved in pretty predictable clusters of light emission.
Perhaps slightly more plausible than aliens is that a large rogue planet collided with a local one and created a debris cloud. Enormously rare, but there are lots of stars and junk out there.
More depressingly, this also matches the kind of "gunsmoke" cloud you get when someone uses planetbuster bombs to reduce a solar system to rubble. (A sunkiller bomb is also a possibility but unlikely because most of those work fairly fast.) This is particularly a concern because one reason for the Drake Equation yielding a sum of zero detections is if L is a very short timespan -- to wit, aliens share the human tendency to blow themselves up.