Part way through the episode the Boatswain disappears without explanation. In the powder store the boy gives him a minor wound on his finger. When the Doctor and Captain return only Rory, Amy and the boy are there, and no one mentions the Boatswain who is not seen again until the final moments. He could not have been taken by the siren as Rory and the boy are also marked and would have been taken at the same time.
When The Doctor and Henry Avery are in the TARDIS, The Doctor pulls the lever on the object with yellow lights down. In one of the shots after this, looking onto the scene from above, the lever has not yet been pulled and in the shot after, it has.
Sailors and ship builders in this period went to great lengths to prevent fires in the powder magazines. The magazine room themselves were often built with a separate lamp room that shone light into the magazine via internal windows so that no flames of any kind would be required in the magazine itself. To have an open flame inside the magazine would be unlikely and extremely dangerous.
The Doctor uses his sonic screwdriver to release the lid of a wooden barrel to let the siren out. It has been established that the sonic will not work on wood.
A stopped heart cannot be restarted with CPR alone, this keeps the heart beating artificially until a defibrillator can be applied.