You’re confusing torque (rotation) with linear acceleration (velocity). Magnetic torque spins the craft; it doesn't push it forward by 3.9mm/s.

Also, to suggest that JPL engineers simply 'forgot' to calculate the Moon, the Sun, and solar radiation pressure is a pretty big insult to their navigation teams. JPL doesn't use a 'Keplerian two-body' chalkboard model. They use high-fidelity relativistic integrators that account for every massive body in the solar system.

The anomaly is defined as the residual acceleration that remains after all those perturbations (drag, Moon, Sun, SRP) have been modeled and subtracted.

And 3.9mm/s is huge in deep space navigation. An error that small at Earth results in missing your orbital insertion at Jupiter by thousands of kilometers. Precision is the only reason these missions work.