From a rational standpoint, I generally subscribe to the selection bias you (and Scriptor in a separate reply) raise as #1. However, for the sake of discussion, let's operate under the assumption these sightings are legitimate/noteworthy.

Personally, I grew out of bothering ant hills when I was about twelve. Nowadays, I pleasantly observe from high above. So why wouldn't aliens do the same?

In this case, your second theory fills in the gaps. But, one would assume some species capable of this technology would also have cultural norms about not interfering with less developed groups. Much the same way we (generally) try not to interfere with primitive tribes around the world.

I suppose, then, that the comparison could be made to the Sentinelese firing arrows at aircraft out of fear and suspicion. The aliens (in my opinion rightly) assume we would do the same to them because they are so foreign to us.