Hay varias maneras de referirse a cantidades.

en... by ...
Vinieron de tres en tres. They came by threes.
Lo comprarón por centenares. They bought it by hundreds.
en... in ...
Estaban empaquetados en paquetes de diez piezas. They were packed in tens.
Siempre los coleccionó de tres en tres. He collected everything in threes.
by ...
Eramos tres. There were three of us.
Eran diez. There were ten of them.