I have been using that map, but based on a couple of Echo Base run videos I watched in the last few days I believe it is wrong. From the videos it looks like the cave in the upper picture is the exit to phase 3. They show the terminal to be right beside the terminal that leads to the lower hanger.
Yes. That bug sucks. That's why i decided to use npcs to enter/exit the Echo Base. From there, I did not have any more problems than in some rooms. Otherwise, it's playable, even if a toon is following you.