Ford did not tell you that, your Ford
dealer did. There is a difference.
go to
www.sema.org and read everyhting related to the Magnussen-Moss act. then go back to your dealer. They have to prove that the intake caused the failure. Now it is possible that it did, depending on exactly what you have done, and how you have done it. If it is the fault of the aftermarket intake, then you are 100% responsible for the repair, not Ford, or your Ford dealer. But, if the intake (or other aftermarket modification) is not the cause of the problem, then it should be covered under warranty.