If the Winter Soldier was responsible for the Kennedy assassination and Magneto tried to STOP the Kennedy assassination then that must mean somehow Magneto lost a fight to a guy wITH AN ENTirE ARm MADE OF METAL
Marvel writers sweat intensely
Canonically in the comic, Magneto has lost to the X-Men. When they had neither Jean Grey nor Professor X (psychics) with them, and both Wolverine (metal skeleton and claws) and Colossus (metal everything) with them. You don’t get more impaired than that against Magneto. I’m sure HYDRA could have found a way.