I ran into this issue a couple of times throughout the game but I didn’t really reproduce it until the very end (because I could progress anyway).
Basically, at the very end, in the teleporter room, my FPS is fine, but if I save the game when the aliens are about to start spawning and then reload that save then my framerate is f***ed. It got to be quite annoying because when I died I had to revert back to the autosave and watch the whole teleporter start-up sequence again. I tried saving both from the menu and with a quicksave but it didn’t have any effect.