NCAA throw in
 

Team A has a throw-in as a result of he alternating-possession procedure. A1 receives the ball from the official and before he/she can pass the ball into the court, A3 is assessed a team control foul. Team B is awarded the ball out of bounds as a result of the team control foul and the official instructs the table to change the arrow. Are the officials correct?

but what would you do in Fed also?

Fed 6-4-5

If the throw-in team violates the opportunity to make an AP throw-in is lost. If either team fouls during an AP throw-in, it doesn't cause the throw-in team to lose the possession arrow.

In Fed, give Team B the ball and the arrow stays for Team A.

Same for NCAA.

NCAA 6-3-4 "Art. 4. A foul by either team during an alternating-possession throw-in shall not cause the throw-in team to lose the alternating-possession arrow."

The officials in the OP were not correct to order the arrow to be switched.