I don't think anybody was surprised to find that the droplets carried different amounts of charge. I mean, we're very comfortable seeing charge act like water ... we know that you can pick up a little bit of charge by scuffing your sneakers on the carpet, but clouds pick up humongous amounts of charge when they rub together and make lightning. Charge can move from place to place, or stick to things, in small amounts or large amounts.
What WAS surprising to Robert Millikan was the discovery, in 1909, that no matter how much or how little charge the droplets had, it was ALWAYS a multiple of 1.6022 x 10⁻¹⁹ Coulomb ! No amount of charge was BETWEEN those multiples. That seemed to suggest that electric charge is NOT like water, but it's more like tiny grains of rice that are all the same size. Charge could stick to things in amounts of 1 grain, 2 grains, 3 grains, 10 grains, etc. But you could never have 1/2 of a grain of charge, or 7.3 . Only buckets of grains that EACH carried 1.6022 x 10⁻¹⁹ Coulomb of charge.