Did you notice these two log entries (my emphasis):
Oct 29: “Wind at East and ENE we weighed at peep of day and turned it through the Gull stream where to my great satisfaction I found the weakness of my Crew …”
Oct 30: “the Isle of Wight bore from us NNW the body of it, but it being cover’d with Snow, Some that ought to have known it better, tooke it for portland.”
Halley was an astute judge of men and in the first entry I take him to be expressing satisfaction that he has identified those members of his crew who are going to give him trouble (in fact some of his officers) and also the reason for it (resentment at having a civilian captain). While in the second entry, Halley appears to be rather defensively asserting his own seamanship against that of the professional sailors, who are here (apparently) at fault.
Oh dear, poor Halley, he hasn’t even left the English coast and is already doing battle with his officers – I’m afraid it’s going to seem a very long voyage!