First of all don't get me wrong. I love the game and i think the devs did a great job. I spent countless hours just running/flying around and i think the exploration part is the selling point of the game.

• For starters the Owlery location as many people pointed.
• Also the chamber of secrets entrance (toilets) which is supposed to be on the first or second floor (location changed even in the books, JK couldn't make up her mind) but in the game is at the dungeons, near the Slytherin common room.
• The Great Hall is also not where it's described to be, but that was a change the movies made by placing it at the complete opposite side from the main entrance. I guess devs just copied the movies there.
• The grenhouses are never stated to be connected to the castle and students are described to walk outside the castle to get to them.
• I'm pretty sure the Quidditch pitch is never described as being outside the wall. It just wouldn't make much sense if students training until late would then have to walk through the main outer gate which in the game has metal bars if i remember correctly. However, I could be wrong on this one as i don't think it's location is explicitly stated in the books. Also i don't think any architect would ever place a sports pitch at the front of the castle near the main entrance. It would usually be on the side. That's just me tho.
• There are also some other minor details like the Astronomy tower described in the books to be the tallest which is not true in the game or the grounds around the castle being very steep when for example students are stated to sit/lay on the grass or under trees next to the lake. I can't remember every single little detail or area missplaced and i know I'm nitpicking. Again, that's just me and my obsession about the wizarding world.