This is a common problem with an extractor. Sometimes you'll even have stains dissapear and then reappear after using the extractor. The problem is that the stains "wick" back up to the surface. After you have extracted an interior, let it dry while working on other parts of the interior or exterior.
Sometimes I will even run the heat in the car with the windows cracked in order to get the interior really dry. You will almost always have some small stains reappear. Buy a quality spotter. A lot of guys use Folex. It's an awesome budget spotter and it is rinseless (very importanat). I'm sure there are good spotters on AG as well. Mist the spots that have resurfaced, with folex. Let it soak in for just a few seconds and then rub the stain out with a white cotton towel. Keep turning the towel until the stain is gone and nothing else is transmitting onto the towel. This will work 95% of the time. It's important that the interior is at least mostly dry. This method works better if the stain isn't soaked.
Some stains are nearly impossible, especially red stains. You will need to do some research to remove more permanent stains. Heat transfer is usually the way to remove red stains. There are special chemicals like red relief, but some guys use a mixture of ammonia and water and an iron and cotton towel.
Don't try this method in a customers car unless you are extremely comfortable with it. You can burn or bleach the carpet. Practice on a junker or scrap automotive carpet.
Good luck!