I think it was when she was at the Freddie Lounds desecration crime scene and was talking about the relationship between the killer and his mentor being a courtship. That was the moment she thought she understood everything about Will and Hannibal (even though obviously Will hadn't actually killed Freddie at all). I…

I beg to differ on this. We saw Alana eating the "breakfast for dinner" that Hannibal prepared for Abigail in season one. And I think it is implicit that Alana has eaten at Hannibal's on many occasions, judging by the conversations we've seen in his kitchen while they prepared meals together.