It would appear, based on what you are saying that one of the bureaus isn't reporting.
Contrary to what one poster said on your question, it's not what anyone is bound by law to let you know that is the issue. The issue as I read it is WHY you only have two scores showing and not three. There is no law that there are three scores. The 3 bureaus, Transunion, Equifax and Experian report scores but, not all lenders or creditors report to all 3 bureaus.
Also, any score you pull from sites like myfico.com are not the same type of reports that lenders/creditors use. We use typically, RMCR's (Residential Mortgage Credit Report). The scores you pull use different formulas and logic and algorythm than the creditors use. Some of your creditors aren't reporting to all three bureaus, and are not required by law to do so. That's why you may only have two scores.
The typical underwriting guideline is to use the middle score of three scores or the lower of two scores. They are required by law to disclose the score used. You have the option of not proceeding with the loan. If it's a refinance, you can change your mind within 72 hours after you close. If they raised your rate, they have to redisclose to you.