I didn't see this happen at all in Alpha 2, so it would seem to be Alpha 3 specific. On the planet screen, it seems to be very picky about where to click to select a hex to build on and same goes for the mouse overs to see the hex bonuses. On some of them I have to hunt around a bit to find where it wants me to click. It's quite annoying.
Also, I know I saw somebody else mention this as well, but I got off to a fairly early start military wise and I've been orbiting the pesky Altaran planets destroying their starports. However I destroy all three of them and a few turns later they've rebuilt them at exactly the same spot. This just gets repeated over and over. I don't understand how they can rebuild them so fast. I'm also not sure if it's intended that they keep building them at exactly the same spots around all 3 planets.