Continuity mistake: When the medical examiner notices that there's something wrong with the brain of the corpse that she is examining, she's making a gesture with her hands but in the next shot she has them by her sides. (00:30:39)
Continuity mistake: In the end when the Kothoga is on fire and chasing Margo, it catches up to her in moments. However, everytime it dramatically changes angles, the Kothoga appears a lot futher away than it was previously, but soon after catching up once again. Noting her progress in the room, this situation is not simply replaying the same scene from different angles. Plus when she gets to the water tank, she has plenty of time to spare to hit a lever, climb the device, and jump in before the Kothoga looms overhead.
Continuity mistake: When the two police dogs, Castor and Pollux, run into the dark tunnels and away from the policemen, one of them, Castor, winds up being killed by the Kothoga. The officer who cared for them, Bradley, goes chasing after Pollux in the dark with his flashlight, and Lieutenant D'Agosta chases after him, with a flashlight of his own. After Bradley finds Pollux, he's talking to him and still using his flashlight, when he gets killed by the Kothoga. However, after D'Agosta gets into that room, there is no flashlight lying on the ground, let alone shining on Pollux - as it fell only moments before.
Continuity mistake: During the autopsy scene, the ties on the medical examiner's mask change between going over the microphone headset and going underneath.
Answer: More then likely, the dog was too afraid of the Kothoga to attack it and when the Kothoga saw this, it let the dog live. The other dog was probably unafraid and tried to attack the Kothoga which prompted it to kill the dog; not out of self-defense, but, because there were still people trapped in the museum and the dog was impeding his attack.