2007 Honda Civic Rear end alignment

I had tires rotated and immediately notice the feeling of skipping and bumpiness. I was told that the rear end needed aligning because the tire taken off the rear had a raised spot in it due to the alignment. I was told that once the alignment was done and the tire was back on the rear, it would smooth out. My question is why does it not smooth out while it is on the front? This does not make sense to me and I wonder if possibly the tire was defective and only became noticible when it was put on the front