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Continuity mistake: Near the beginning of the movie, when the young adult Henry attempts to stop the British Captain from sailing into the triangle, Henry is subdued by the Marines. The British Captain accuses him of treason and rips both of Henry's sleeves down from the shoulders. The next camera view is from slightly further back as the British Captain commands the Marines to take Henry below and Henry's sleeves are still intact.
Answer: He's probably worried that either the crew will attack or at very least frighten Henry. Or he just doesn't want Henry to see how horribly the curse can affect people.
But because Will is ferrying souls to the after life, like Davy Jones should have done for the full time, he was captain of the Dutchman. There is no curse that would make the men look like sea monsters. They only started to look like that because Jones denied his duties after 10 years of service, when Calipso didn't show up. So the crew would look like normal men, so Will being worried that Henry will be frightened by them, can't be the reason he started to panic.