When Harry and Hermione use the Time Turner in the hospital it is "10 minutes to midnight" because thats the time that Dumbledore locks them in the hospital. But when Hermione is explaining to Harry, the clock strikes 6.00 (and there is sunlight streaming through the windows) and Hermione tells Harry that they just went back in time, 3 hours back. 3 hours back in time from midnight is 9pm, not 6pm.