Since the graphics data for BP is in the code, this may be the result of an unwanted glitch. But the code for the city is very simple (just four code locations: one for initial pattern load, two for scrolling back and forth and one for displaying) and I cannot see anything which could create a gap in the city.
The terrain CTRLPF write at $F761 would seem to be a possible candidate (the reversed building gfx makes the scroll happen from and to the center rather than the edges). But the value is an immediate value, and the register is updated just before drawing the city on every frame...so it would take ROM corruption for that to happen.
IMO it was an embellished account of the actual EE. Pretty common BITD when mythbusting was difficult.