Basically after I complete the mission unknown caller (getting the hotline) and am going to see Anti I run into this bug. I can get into the control room from the start and access that control point. Also some enemies don't spawn, and the chest throughout the level are already looted.

Did you start a new game after having already unlocked all the stuff on that level? I had this happen on my second play-through. I don't think the game correctly resets itself when you start a new game, so some parts of the old save leak through.

I was able to fix this by shutting off GOG Galaxy cloud saves* and deleting all the files in C:\Users\<username>\Documents\My Games\Control\Saves. Deleting everything will completely reset the game.

*not sure if this step is strictly necessary, but I didn't want to take any chances of the old save reappearing from the cloud.