At about the 30 minute mark Flint places his pistol on the desk and sits down against the wall. When the camera pans back to show the entire room, the pistol is not on the desk.
At around 17:40 Flint states that their captors wish to interrogate them one at a time "...to see if our stories jibe". To "jibe" in sailing terms refers to course alteration by design in order to maintain SOG while tacking. The usage of the word with the meaning "To be in harmony or accord" is an Americanism that did not originate until the 1800's. As the setting for Black Sails is the early 1700's that word, in that context, would not have been used.
At the start of the episode, the quality of the black pearls is being checked at night, in the dark, with no obvious light source close at hand and very little ambient light. They would have been almost invisible.