The following from the brief seems to me to be MNTA's strongest argument by a long way:
The word “solely” in the statute makes clear that even if the patented invention is used for a purpose reasonably related to the development and submission of information to the FDA, other uses of the invention are not protected under the safe harbor. For example, a drug manufacturer may use a patented invention both to sell a drug commercially and to conduct a post-approval clinical trial. The clinical trial is protected under the plain terms of the safe harbor. But use of the patented invention for commercial manufacturing and sale of the drug is not exempted from infringement liability because such use is not reasonably related to the development and submission of information to the FDA.
Here, Amphastar’s “infringing activity is not solely for developing and submitting information to the FDA. Instead, Amphastar uses this method for the purpose of manufacturing a product to sell on the market in commerce
It boggles my mind that the court below dismissed this argument.