His Last Vow - S3-E4
Plot hole: Sherlock manages to convince Janine to let him into Magnussen's quarters after deceiving her into thinking he is going to propose. Several days later, she is enjoying her "revenge with profits" on Sherlock for his duplicity. Problem: There is no way she could have found out. She was out cold moments after letting Sherlock in, and Sherlock himself was shot by an assailant, which he had misidentified. Only Watson knew Sherlock's true intention, but we know he did not reveal it. The shooter and Magnussen did not know and had no opportunity to tell Janine anyway. (Plus, Magnussen's credibility is too low.) In fact, if I were the director, I wouldn't bother making up a motive for being a "grasping, opportunistic, publicity-hungry, tabloid whore" (film's own quote). Such a person loves "profits", not just "revenge with profits." (00:31:00 - 00:43:00)
Over My Head - S3-E4
Plot hole: Daphne was able to hurt Duke because his name appears on her cell when he called, but names only show up on a cell phone if the person's number and name are programed into the phone, and Duke has already said he doesn't know her.
Plot hole: Episode 1: All passengers on cruise ships have a passenger card with their name and cabin number imprinted. They are not just identical key cards like in hotels.