You need to make sure you visit the two small recesses in the two caves (behind cellar and under pantry).
You need to visit the 4 vent rooms. There's a vent in the pantry, study, bathroom and upstairs landing.
You also need to click on the tree in the middle of the garden and the grave behind the shed in the garden.
All the other rooms you will need to visit at some point in the game to progress. The above are the ones you might miss.