The problem is that we, external observers, are all-knowing. We know that clones has to learn things and just asking the right question is a solution. But Twilight didn't know what clones didn't know, so she couldn't find such answer in short time. Another problem is: what if Twilight asked a question that one clone answered correctly but real Pinkie Pie didn't (e.g. because of stress)?

I've already commented on this:

The problem is that Pinkie has a photographic memory, and so do the clones. The real Pinkie gave the clones a crash course on her life story, and knowing Pinkie’s motor mouth she can teach them a LOT in a short amount of time. Add onto the fact that the clones learn more and more about Ponyville and Pinkie’s life with each passing second, and the quiz would’ve been so long that the clones would start slipping out of town hall before Twilight can quiz all of them. Sure, it only takes one wrong answer to find a clone out, but it can take quite a while for any given clone on a random test to actually give a wrong answer. Adding onto THAT addition: once one clone gets a right answer, ALL the clones know that answer now (photographic memory). Unless you quiz them individually in a soundproof room, but that'll take even LONGER