After the Mutant leaves, having secreted a large amount of mist from its neck, close to Dr. Beckett, the next shot immediately zooms out and there is no mist in sight.
The blue lights that they use are only good for marking locations. They don't cast any usable light for seeing your way. They would actually make the users vision much worse as they will dilate their pupils ruining any natural night-vision.
About 26 minutes, when inside the structure there is a great deal of light showing through the slats, though it is night and dark outside.
Colonel Sheppard is the military commander on Atlantis. As such, he would have signed off on all team assignments and carried out regular reviews with team leaders. There is no way he could be unaware there was an all-female team under his command.
Upon finding the gas mask, the team should have left the catacombs and called in a hazmat team. They wouldn't just ignore such an obvious sign of danger.