"As for Kirk, Spock & McCoy's trip through the hallways at the start of the episode, I always assumed that the second corridor sequence was some distance away from the first, probably inthe secondary hull as they made their way towards the Hangar Deck. Certainly they do pass a sign directing them back toward the "Transporter Section" which (as you've suggested elsewhere) is likely to be in the same hull as the Shuttlebay."
The DP of "Journey to Babel" definitely made some odd choices.
The scene you're describing, IMHO, takes place in the saucer because next we cut down to the security detail in front of the Hangar Deck and witness Sarek's shuttle landing, giving our triumvirate plenty of time to finally arrive in the engineering hull.
Another corridor oddity is the strange shot of the circular corridors in "The Alternative Factor" (Lazarus strolling around). Judging by the editing he walks through an "H" corridor assembly where the upper and lower edges of the "H" are bent outwards. Maybe a corridor connecting two adjacent corridor circles.