The Time-Turner only allows you to travel back by multiples of 60 minutes.
The smallest unit of time that you can go back by using the Time-Turner is one hour. The next option after that is two hours. The Time-Turners have no capability to travel by units of time which are smaller than one hour. Time travel is done in multiples of one whole hour. That's just the way it works.
So, for instance, using three turns...
"I am going to lock you in. It is -" he consulted his watch, "five minutes to midnight. Miss Granger, three turns should do it. Good luck."
(Prisoner of Azkaban, Chapter 21, Hermione's Secret).
...takes you back exactly three hours...
"We've gone back in time," Hermione whispered, lifting the chain off Harry's neck in the darkness. "Three hours back..."
(Prisoner of Azkaban, Chapter 21, Hermione's Secret).
Similarly, JK Rowling has added information on Pottermore which says that Time-Turners are powered by magic that works one [exact] hour at a time.
According to Professor Saul Croaker, who has spent his entire career in the Department of Mysteries studying time-magic:
"As our investigations currently stand, the longest period that may be relived without the possibility of serious harm to the traveller or to time itself is around five hours. We have been able to encase single Hour-Reversal Charms, which are unstable and benefit from containment, in small, enchanted hour-glasses that may be worn around a witch or wizard’s neck and revolved according to the number of hours the user wishes to relive."
(Pottermore, "Time-Turner").
Therefore, if Hermione comes out of her lesson at 11:58 then the latest that she can travel back to is 10:58. The next-latest option is 09:58. She cannot travel back to, say, 10:45. If she were to go back to 09:58 then that would leave her with a whole hour to kill. What's the point in that?
Consequently, in the books she travels back exactly one hour each time. She then has to rush to make up for the time that she spent finding a discrete place to use the Time-Turner. That's why she was always late or in a hurry. In addition, she may well have had further to travel between her lessons than Harry and Ron did - or the travel time which is factored in for other students isn't for Hermione because of her unusual timetable.
All this assumes hour-long lessons, which runs contrary to the running hypothesis that Hogwarts lessons seem to last 45 minutes. However, if we assume the timetables give 45 minutes teaching time and 15 minutes for students to travel between lessons then lessons would still be spaced at hour-long intervals. Which means that the one hour that the Time-Turner gives Hermione for moving between classes is sufficient, if only just.
In fairness to Hermione, she wasn't in the habit of walking into lessons halfway through. She was just often flustered and out-of-breath when she had no obvious reason to be.
Movie answer
The books are consistent that one turn equals one hour of time travel. Alas, the movies are less consistent and since the question cites the film I thought I'd answer in relation to that. In the film, Dumbledore still locks them in the hospital wing at midnight.
On cue, the MIDNIGHT BELL begins to CHIME... DING!..
They still turn the Time-Turner three times.
DUMBLEDORE: Three
turns should do it, I think.
Yet they end up traveling back to 19:30!
HERMIONE:
Seven-thirty. Where were we at
seven-thirty?
HARRY: Huh? Dunno...going to Hagrid's?
They travel back by four-and-a-half hours. So, as far as the movies are concerned, one turn of the Time-Turner equals...one-and-a-half hours? I can only presume that that's how the film-canon works.
To confuse things more, when Harry and Hermione are running back to the hospital wing the huge clock on the wall has a hand pointing to twenty-past (2:06 below)
I'm assuming this is the second hand (not the minute hand or the hour hand) since it's striking for midnight. But this is also unclear.
Perhaps the confusion about how the Time-Turner works in the movies is due to an attempt by the filmmakers to marry the turns of the Time-Turner (one hour) with the length of the lessons (an hour-and-a-half) - to make them the same length. This may be giving the film-makers too much credit. For whatever reason, though, one turn in the movies seems to equal 90 minutes of time travel.
This would still leave Hermione with the same quandary when it comes to travelling between lessons, however. If anything, she'd be left with less time than she would in the books. If a double lesson is 90 minutes and the Time-Turner sends her back by 90 minutes then that leaves her with next to no time in which to move between classes.
