Some of that forced, unnecessary awful dialogue that Glados says during the elevator rides when you're both progressing through Weately's test chambers.

the morality cores were taken off of her and her voice changed to similar to what it is now

The signs that are near the sealed off sector of test shaft 09 that say it was sealed off on June 16, 1961. This date doesn't make sense to me. These signs are at the beginning at the very bottom, but they are also at the very end right before you see Wheatley again, after you've passed through the 80s and 70s areas. I get the impression that different parts may have been sealed off one by one, but if that's the case there should be different signs. Keep in mind that certain areas in the shaft were built in the 70s and 80s. If they sealed off the entire shaft in 1969 then maybe they would have removed those signs expaining that it's been re-opened????

This is starting to get confusing, probably because they didn't really plan out the building of the entire shaft. They just sort of made it so the bottom was built first, and as you go upwards you go forward in time. This makes for a nice story but doesn't make as much sense. There's a whole lot of confusion for me regarding exactly when each part was sealed and re-opened.

Why is the Borealis drydock 3 kilometers underneath the surface of the Earth? The only solution I can think of is that...if this dock was part of some kind of gigantic underground tunnel/airlock system- perhaps they can raise and lower the water level, and there is a long underground tunnel leading all the way to the nearest shoreline and then a gigantic shaft where they can raise and lower the water level by pumping the water out or in in order to bring the ship to the surface and back, but then then why was there an entrance that would have been well below the waterline, and why would this lead to the offices from 70s Aperture? (which is the entrance we go through to see the life rafts that say "Borealis")? If the area can be filled up with water, then if someone left the door open water would come rushing out past the offices and into test shaft 9, flooding the entire underground area.

the graphics from the brainwashing scene.