A Molded Case Circuit Breaker (MCCB) consists of 2 basic parts: the switch and the trip unit. "Frame Size" refers to the switch part. So if you have a 250AF, that means the switching element is rated for 250A. But on that switch element you can attach a trip unit that is 100A, 125A, 150A, 175A, 200A, 225A, and 250A. If on the other hand you have a 125A frame, it may have trip units that range from 15A to 125A. The "rating" of the breaker is generally considered the trip unit rating, but sometimes an engineer will specify a frame size because there is usually overlap, as indicated above, and he wants to make sure that if some day in the future that needs to be a larger trip unit, it will fit.
So for example take the term "125A breaker". That could be a 125AF/125AT or a 250AF/125AT. Both are legitimately "125A breakers", but if they are in a panelboard, the "strap kit", the bus connectors that attach the breaker line side to the bus bar, is totally different and the width of the breaker is different. So if at a later date it was determined that you want a 150A breaker in there (assuming a new set of conductors of course) and you had a 125AF/125AT breaker in there, you might have to rearrange the entire panelboard to make room for a 250AF/150AT breaker. If you had a 250AF/125AT to begin with, no big deal.