![Blocks][1]

I'm guessing your FBD looked something like this, where $F_1$ is the external force you apply. I'm assuming here that the top and bottom block don't slide relative to each other, so the forces at their junction ($F_2$) are equal and opposite.

The net force on the top block is the force you apply, $F_1$, minus the frictional force the bottom block applies to the top block, $F_2$:

$$ F_{top} = F_1 - F_2 $$

Because $F_1 > F_2$ the net force $F_{top} > 0$ and the top block accelerates.

  [1]: https://i.sstatic.net/ghe2x.gif