The movie version of Harry Potter and the Prisoner of Azkaban really emphasizes time and clocks, which is quite fitting because Book 3 will probably always be remembered as the Harry Potter book with the time travel. Though it's downright tame compared to Lost (Hermione turns an hourglass, not a donkey wheel), this time tinkering is still pretty trippy. Harry and Hermione live out a time loop where everything somehow fits together in the end like a jigsaw puzzle.
But time and its progression is far from neat and tidy and predetermined here. Time can seem impossibly, cruelly slow – see Harry waiting for his Firebolt or Sirius's interminable twelve (unnecessary) years in Azkaban. Time can be also insanely fast – see Hermione's jam-packed schedule or the meager time allotted to save Sirius. And time can be taken away as well – see Harry's lost time with his parents or Sirius's lost adulthood.
It's fitting that the Time-Turner doesn't fix everything in the end; though Harry and Hermione use it to free Sirius and Buckbeak, they can't use it to clear Sirius's name. As the kids learn, time is what you make of it, and having more or less can be both a good and bad thing. So it comes as little surprise that Hermione returns her Time-Turner at the end of the year.