Coach-
I think your assessment is right on the money. Had they discovered the error while Team A was still shooting the erroneous free throws, they could have corrected and then given the ball to Team A for inbounds. As for the original scenario, Team A is actually being penalized for the error by not getting to inbound, and also having the free throw points taken away.
I think to sum this up, it goes to show why good communication with your scorekeepers is critical. Hopefully, these situations can be avoided before they even happen.
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Coach, Don't Shoot The Messenger!
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