What evidence led thomson to propose that the mysterious negative particles he was studying were smaller than atoms?

Thomson calculated a charge-to-mass ratio for the electron that was almost 2000 times greater than that of a positive hydrogen ion – the smallest particle known at the time. It made sense to Thomson that the magnitude of the two opposite charges should be equal which meant that the mass of the electron must be approximately 2000 less than the smallest atom.

The problem here is that according to aufbau principle before 3d orbital 4s subshell comes.after filling 3p orbital with electrons you have 4 electrons left, you place two in 4s with opposite spin and the other two in 3d in any of its two orbitals of total five orbitals with the same spin.