There are times when you run your credit and it actually comes up with no score, which sometimes shows as a lot of zeros. This is generally when you do not have enough credit.
What I recommend you do if you want to get pre-qualified for a mortgage, is speak to a reputable loan officer, possibly try a few to see who you click with. Choose one of those only to run your credit. They will get you the scores that will be used for underwriting purposes, not the scores you get when you run credit on yourself.