Yes, all VIN's should match. Not uncommon though for Ford to make VIN mistakes. I had a '66 coupe 289 that I drove daily from 1981-1989 that the VIN on the drivers side apron and the VIN on the drivers door was off one letter, the engine code on the door was T(6 cyl) and the one under the hood on drivers apron was C (289,V-8). All the rest of the VIN matched.
Also, I read in Mustang Monthly back years ago that approximately 50 vehicles(Mustangs,fairlanes,etc) on the assembly line was stamped with the same VIN.