I agree with 
@Eggcessive. It's possible she inhaled feed dust or dust from shavings. I've had it happen. You can put a little water in their feed to make a mash to keep feed dust to a minimum. Try not to use shavings from the bottom of the sack where small particles and dust settle.
It would be best to put her back with the others. I've added 3 day old chicks into a group of 1.5 week old chicks in a brooder without any problems at all, that's not a problem.
One possible issue could be your attempts to use deep littler method with your chicks. It might work for your adults, perhaps not with chicks. Personally, I'm dead against deep litter method.