I am at the same spot, I have not been spotted once and I can't get into the tunnels. Rather irritating, I am going to try and go get Annie and head back to the tunnels, see if that helps.

Didn't help... still stuck. I attempted to enter the tunnels with 0 of 4 alerts and 3 of 4 alerts.

I encountered exactly the same error and took a look through the console and debug output.

For the bug that you could not enter tunnels my console said that "scene could not be loaded for map" or something like that. Maybe the scene file has the wrong name or doesn't exist.

By the way:
If you get spotted and fight of the cult goons a message tells something about Dr. Hansen.
The Dr. Hansen message confused me because I killed him in Everest Museum.
After that Annies starts nagging at you about something that happened to Coyote (even though coyoe still lives or isn't a Party member at all). Annie might be supposed to run with you but is stuck on the Helicopter map.
According o my console output a party check error is encountered because the number of civilians doesn't match. This might be because Annie is registered as an civilian.
So Gevrik could register her as Shadowrunner with the playercharakter as master and, if necessary, port her to the group. Ths should handle the problem that Annie couldn't leave the helicopter map, imho.

I hope this problem will be handled soon, because I can't go on too.

way late to the party on this one, but I'm having the same issue now. I can't seem to find a solid answer anywhere about this, has anyone else found anything?