It sounds like he's promoting Frederick to Anne. Since Benwick would have stayed at Kellynch with the Crofts on the visit that never happened, the Admiral might have gotten an inkling from Sophy that perhaps Benwick was interested in Anne.

I think the misunderstanding could be seen either as evidence of his inability to be subtle and engage in subterfuge, or just his way of promoting Frederick to Anne, with a view toward matchmaking.