$50 per opening is a very reasonable price to cover exterior trim. We charge $70 per opening, regardless of whether we have to add furring or framing to the existing opening. It costs more the way we do it, but we don't charge extra when we have to add brickmould and such. The only thing we charge extra for is replacing rotton sills, which is usually $30. Sometimes you don't find out the sill is rotton until you remove the storm window or the old cladding- that's a case of charging for something that was unforeseen.
If your contractor knew he was going to have to charge extra to add framing around the perimeter of the opening BEFORE it was clad, he should have figured that into the bid and mentioned it up front. Either that, or it should be included in the cost as you suggest.
Now, it's also possible that you have misunderstood what he said. He may have indicated that "it costs more to get aluminium windows out because you have to cut them out." In your mind, you may have thought that meant "they are harder to get out". In his mind, he is thinking, there is more labor and framing involved than the standard $50 cladding fee would cover- you have to cut them out and there is nothing to wrap with aluminum trim coil. All that must be added before it's clad. With other types of windows, that's already there. It sounds like you have misunderstood what the extra $50 was going for.
Most often, I've found that's the case- the contractor knows what he's bid and understands what it will take to complete the job, while the homeowner doesn't understand the entire process completely but signs the contract anyway, hoping that the contractor knows what he's doing and is being fair about it.
If he's changing his story, that's another matter.