Had this issue several times, but it was months ago. I thought it was fixed , but I didn't find myself in this scenario lately, I use to either evacuate 30-60 sec before launching the thing, or they stay and die. It's more the latest to maximize the chances of not getting the Halley getting disabled during the moon's course.
I regulary evacuate moons shortly before impact. Not way for them to do anything 10 seconds before it is too late. I never had such an issue. So chances are it's a irregular bug. The Lobby ID's are really important to figuer out what those games have in common.
Just tried to repro bug 4076 (purely out of curiosity) and it's still present in 71937: Bots and vehicles being carried in an Astraeus in orbit can fire on and destroy structures / units on the ground. This can be seen in 12645088213139473730 at around 73:44. Added a comment to the bug with full details.
One note - how much memory do you have? Because you're using integrated Intel graphics, if you have the min Mac Mini spec at 4GB, your memory may be running out - since your graphics card is going to be using up a good portion of your memory. The latest 10.8 should be able to run the game, though Intel Integrated 4000 is close to the min spec the game will run on.
This broke the game for me. Launcher now no longer plays the game. I've tried deleting everything and starting from scratch yet I get the same error. I've made a separate thread.
Good thought on the memory. As a web developer I know I need a lot of RAM, so I maxed it out at 16GB. The game shouldn't even scratch the surface of that. The graphics card did concern me with the minimum specs, but the game plays okay on medium details with shadows off, and ambient occlusion off. I'm probably going to tweak the settings to take it even lower to see if that helps fix the issue.
I just noticed if you go down low using the free/debug camera the atmosphere gets clipped: Edit: Apologies for being lazy (as SXX said below) it's an old issue: PA#838.