When you hit the scene where the two aliens start arguing and after you use the Look and Think options, two more options appear. The third, "Run Away" takes you right to the map where you can only get the bad ends by running into the aliens, all the spots with unique endings are locked out. That's likely what you're experiencing. Instead, you want to pick the fourth option, "Listen", and have the aliens explain their backstory. When you exit to the map after that, the locations like the factory are opened up.