Yes, but they should be within a few points of each other. If they do differ by more than a few points it should be a red flag that something is wrong and should be further investigated.
There are three different FICO scores developed at each of the three different credit reporting agencies. FICO uses the same method to come up with each score, but the score at each of the three agencies may not be exactly the same because of the different ways lenders report information to the agencies. The FICO score from Equifax is called BEACON, the score from Experian is called the Experian Fair Isaac Risk Model and the score at TransUnion is known as EMPIRICA.