Count the basket?

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Had a situation last night and I need some guidance. I am T, middle of the 3rd quarter (Girls Varisty...not that it matters). A1 puts up a 3 point attempt and while the ball is in the air my partner calls A5 for a push. The attempt was good and I give the signal as my partner is coming out, waving his arms like a windmill in a hurricane. He waves off the basket and awards B the ball for a spot throw-in on the baseline. I thought the basket should have counted but at this point A was up by 35 and it wasn't worth getting into a debate...especially since the coach for A didn't make a sound.

After the game my partner didn't want to discuss the play. My rule book wasn't in my bag (that mistake has been corrected) and I forgot to look when I got home. Should the basket have counted? It was clearly in flight when the foul was committed.

Thanks,