Oil drops are inherently neutrally charged but by passing them through X rays he ionised them.
Hence there was an excess negative charge resulting in the oil drop to become negatively charged.
It's this negative charge that Millikan measured right? Like the excess negative charge.
I've heard that this notion is as universal as the timeless messages Shakespearean texts emanate and send students into a purgatory that not even Eliot's hollow men have experienced.