This is what my PDA map looked like after getting this quest. The waypoints look clearly broken.
(Right click > Open image in new tab)
The major problem is that after seamlessly traveling through canals and reaching Pripyat I don't get any assignment from the military, which from what I read I think I should. Hotel room 26 doors are also closed, so I can't progress the story.
Maybe someone knows some kind of console command which will let me start the military quest? Any other solutions are also welcome.