Continuity mistake: When 9 created the "torch" from a light bulb, it needed to be turned to work. However, when 3 and 4 investigate the bulb one of them simply puts it in and it starts glowing without being screwed.
Continuity mistake: During the funeral scene for 2, a tunnel with steel bars is seen in the background, with none of the bars broken. When the camera angle reverses once 2 has floated into the tunnel, one of the steel bars is broken.
1 tells 9 that he led the others to their current hideout, which he refers to as "sanctuary". The building happens to be Notre Dame church, famously referred to "sanctuary" in "The Hunchback of Notre Dame."