Well it's impossible for us to know what the exact differences are since we're not in your school, but I'm going to assume based off just the names that mammalian physiology is all about...well, the physiology of different mammals. In my school I took a class called animal physiology that discussed the physiology of different animals (mammals, fish, reptiles, amphibians, etc.). It discussed how different animals breathe, regulate heat, how their body deals with acid/base regulation, different hormonal functions, and more.
Anatomy and physiology at most schools discusses both the anatomy AND the physiology of humans and/or other animals (in my school, they discussed anatomy/physiology of cats as well). For example, I never learned the names of different muscles/tissues/bones/body parts since I never took A&P. This is what you'll learn in that class, along with some physiology.
A&P is probably the more interesting of the two if I had to guess. Probably a bit harder of a class though.