Doppelgängers can be compelled if they are human.

In legacies they said that supernatural beings cant be compelled

Doppelgängers are mystically recurring spurred by Nature. They are and aren't supernatural whenever the plot demands it. I.e. Stefan is a Doppelgängers and was compelled by Katharine.

In the beginning, it was supposed to be just a human being on TVD, the mythology of the Doppelgangers was being formed from the 2nd to the 8th season, with the whole history of blood loaded with magic and the history of nature that made them like copies.

Doppelgängers are a supernatural Occitan was. Or being, if you prefer. And they can be compelled. Klaus compelled Katherine. Damon compels Elena, as does Alaric.

Technically, the only supernatural thing in them is their blood. Thus, they are not sufficiently supernatural to be immune to compulsion.

I think its because Elena is a human doppelganger, she's not a vampire at that time.