Are we sure that all of the Timeturners were in the ministry that night though? In "The Beetle at Bay" chapter 25 of book 5 we find Umbridge inspecting every lesson of Trelawny's and Hagrid's. How was she doing that plus teaching her own classes too? Could she have had a timeturner? If she did then after she had her day with the Centaur herd was it on her, or was it in her office? It's not explicit that she returned to her office after the centaur incident, we know she made it to the hospital wing... but nothing else. If it was still in her office would it have stayed there until the following year when, possibly Snape moved offices (sorry, I'm being slack and not looking that up) so Slughorn could have the potions one.