fouling without the ball

I was at a game on friday and a 3 point shot was taken and went in, while the ball was in the air the base line ref. called a foul underneath the basket. the 3 points was good, and they gave the ball to the shooting team on the side.
I had 2 refs sitting next to me 1 argued that even though it was'nt a 1 and 1 he thought the kid under the basket should get 1 shot even though he did'nt shoot the ball in the first place. Please help
who knows this call ....

Cody,

Team A has the ball.... player 1a shoots and makes a three... correct? Player 2a gets fouled... NO 1 & 1 situation.

Why should 2a get a free throw?

On a defensive foul other than one against an airborne shooter, regular bonus rules apply, unless intentional or flagrant.

In this case the fouled (scoring) team would get the ball out of bounds.