First up, read the stickies! Specifically this one.
1. Already reported. Go post your save in the appropriate thread.
2. Ooh look, already reported as well. Go post your save in the appropriate thread.
3. There's probably an alien base you haven't found yet causing that. Too bad you didn't post a save so someone could check.
4. Strangely enough, I've had no problems with this. Perhaps you've found a bug? Check the threads to see if it's been reported and if it hasn't, make a new thread for it following the guidelines posted here.
5. Have I said 'known bug' enough times already? I didn't think so.
6. If the aliens in question are Androns, this is a known bug. Or perhaps a feature, I'm not sure.