This isn’t a plot hole. This is very specifically addressed in the book. First: Harry DOES see Moody in the Marauder's Map. More than once. Harry notes on more that one occasion that “Moody is in his office again.” Why would that make Harry suspicious? Harry sees other teachers in their respective offices all the time. The Map is a contraband item, and Harry usually only uses it when he’s on his own, so he wouldn’t pull it out in the middle of class to verify that the Moody in the classroom is the real one. Second: The map does not distinguish between Barty Crouch Jr and Sr. It only says ‘Bartemius Crouch.’ At the time, Barty Crouch Sr was a judge on the Tri-Wizard Tournament, and had every reason to be at the school. He was also famously against ‘Dark Wizards’ and a high up ministry official, so Harry wouldn’t suspect him of being a spy for Voldemort. Third: JK Rowling specifically addresses this and uses it as a clue that Barty is Moody in disguise. It’s subtle, but it’s there. One night, Harry is looking at the Maurauder’s Map. He sees Moody in his office (again). He then sees Bartemius Crouch in Snape’s potion cupboard. At the time, Barty Crouch Sr. was supposed to be too sick to act as a judge, so Harry wonders why he’s at the school. He runs to the cupboard. By the time he gets there, Barty has left, and Snape catches Harry. He accuses Harry of stealing the potions supplies, supplies that are specifically for Polyjuice Potion. Snape pulls out a vial of Veritaserum (truth potion) and threatens to question Harry. Suddenly, Moody shows up and bales Harry out. During the first reading, you’re so relieved that Harry got out of trouble, that you don’t really question why Moody showed up all of a sudden. It’s not until you re-read the scene that you realize that Moody never left his office. It was Barty all along, who didn’t get far from the the scene of the crime. When he thought Harry was going to be questioned with truth serum (and expose that he wasn’t really the culprit) he swooped in to put a stop to that. Finally: Harry tells Fake-Moody that he saw ‘Bartemius Crouch’ in his Map and he thinks Barty Crouch Sr. is the one stealing the ingredients. Fake-Moody acts impressed and asks if he can borrow Harry’s magical map to help find the “spy.” Harry gives it to him. So, Harry doesn’t have the Marauder's Map for the rest of the school year. He doesn’t get it back until the teachers expose Barty Jr. at the end of the year. To summarize, it definitely isn’t a plot hole, since the text specifically addresses this issue, and even uses it as a clue to Moody’s true identity. I can’t speak for the movie, however. I can’t remember the events of the movie well enough, but I know they condensed several scenes, and may have cut out Harry seeing Moody in the map in the movie.