Portals moving would cause reality problems, and so the game cuts any portals that do so. However one level requires you to put portals on moving surfaces.
Despite the facility being all but shut down after G.L.A.D.O.S. was 'killed' the first time, the facility upgraded features such as the elevators.
A crow would never fly into and lay eggs in an underground complex that may be miles under the surface.
While it is true that potato batteries do exist in the real world, no potato battery would ever be strong enough to power a functioning computer that housed GLaDOS' AI with that she can use to listen and talk with.
Given that the facility has been abandoned for years, the potato batteries should have rotted.
When GLaDOS first awakens, she uses mechanical pincers to lift up the player and Wheatley off the ground, crushing Wheatley and dropping the player into the testing course. Strangely though she never tries this at any other point throughout the entire portal series despite its effectiveness. Not even during the first boss battle against her.
The facility is so deep that building it should have taken at least 50 years or more.
During the first core transfer, Wheatley gets his handles removed when he gets put onto GLaDOS' body. However, in the final boss battle against him, his handles somehow reappear in the cutscene right after the player shoots a portal on the moon, where the player holds onto Wheatley's handles to avoid getting sucked out into space.
At one point in the game GLaDOS says that she will live forever while Chell would die in sixty years or less. GLaDOS was "killed" in Portal and still refers to the event with phrases like "since you killed me" and "after you murdered me".