I would like to second this. It was a problem in GC2 as well. Which reminds me of another one from GC2, which I haven't payed much attention to in GC3 since I have mostly played small maps, so it's not much of an issue. Ships set to "auto explore" would chase in similar directions, especially if there was only one unknown sector nearby. Even more annoying however, was that none of the ships took their "sensor range" into account, and would simply pilot along the edge of known space, wasting half of their sight, instead of piloting within unknown space to maximize their view distance in both directions. This is especially problematic with scouts early in the game since their sensor range is so small. If any ship should be able to pilot in this manner it is a "scout" ship. 

I have noticed this problem as well,  and have been doing as RadioBlues said, at least to get them started, but they still end up chasing the same anomalies or unexplored space. And I thought this problem had been solved in GC2, but I could be mis-remembering. Please have the code for autoexplore and autosurvey check were other ships are going before assigning destinations.