The rust observed on the shackles is purely cosmetic and does not affect the strength of the shackle or the operation of the padlock. Rust is normal for Boron steel in certain environments, especially marine environments.
In the design of AP3, we faced a choice of using a weaker stainless steel that would not corrode or a stronger boron steel for the shackle. We chose Boron because we believe it is more important for the locks to work and be strong than it is for them to be pretty.