In method of treating claims, they most certainly can be. Let me explain.
Product-by-process limitations are used to define a structure or composition by the process used to make it as opposed to the structure or composition itself. This can be very useful when a structure is not specifically known (e.g., a polymeric composition). However, if the structure or composition was known at the time of filing, the product-by-process limitations are not given any weight. They're literally ignored. Biogen MA was awarded a patent that claimed the use of a recombinant interferon-β product for the treatment of Multiple Sclerosis. The product, a recombinant polypeptide, was defined in terms of how it was made (via a non-human host). Biogen MA then sued EMD Serono, who was marketing a competitive product, for infringement.
The CAFC held that even though the product-by-process limitations were nested in a method of treating, the standard claim construction rules held. The product was known, therefore the product-by-process limitations were not considered. Biogen's patent was considered anticipated and therefore invalidated. So, the product-by-process strategy got Biogen a patent, just not an enforceable one.