Ok, so I have a big giant custom city map. Your character enters the city, and I set up a 'Complete All' section where you have to explore the city and ask around before continuing. You ask the two people, and then you get the mission to head to a specific building. You go inside, you do some stuff, kill some people, and find out you need to head back out and to another building. You head for the exit, get outside and:
The Complete All text pops up with the mission that started you on the map. Away team officer says the same stuff, Mission Text on the side now says Go Talk to So and So, etc. The only difference from the first time you did this being that it does accurately take you to a different spawn point, specifically the one outside the front entrance of the building you were just in, rather than the entrance to the city.
Now I've had transitions back and forth between maps like this and never had a trouble. This is the first time I've used a 'Complete All' section though, which is why I've narrowed it down to being that problem.
So my guess is that when you re-enter the map, the program figures you must complete these things before continuing. (Despite the fact that it was much earlier in the story).
Now, Devs, does this sound like it's plausible or could it be something else?
You have used the same map twice in the same mission.. You will always get strange loops like this no matter what you try. You must make different copies of the same map for each time you enter or leave.
Unfortunately for you your giant map will only be good for one use until a copy map function is added. I have managed to re-use maps in different missions by importing a published mission and renaming it. It saved a tremendous amount of time and hassle, but won't help you out much...
This is probably why you should only make what you reasonably need to get your mission to play and function well. At the moment you've probably thrown a lot of time and effort down a Foundry Rat Hole.