A1 is fouled on a try & we awarded 2 FT's since the try was missed. As I finished reporting the foul to the scoretable, coach of A called for a timeout. Sub A6 then reported to the scorer after the first horn so we did not allow her to enter. We then administered first free throw, then sub B6 reported to the scoretable. We motioned in both A6 & B6 before the 2nd free throw. Coach of B then got mad and said we could not allow A6 to enter until the clock had started since she didn't report until after the 1st horn, but said his girl could come in because she did not report as part of the timeout. After a heated discussion (on the coaches part) we allowed both subs to enter before the 2nd free throw since this was the next opportunity to enter the game and if one sub is allowed to enter then all subs should be able to enter. Right or wrong?

Definitely allow the sub!!! You were correct. That coach was OVER-COACHING. He must've thought he heard or read something somewhere and was really pushing it. This is a common sense decision. Unfortunately not all coaches have this... If anyone else out there thinks otherwise, plz let me know!!!
You sub at the next opportunity which was before the 2nd free throw.

you got it right. Agree that the coach was overdoing it.

The only players that could not return until after the clock started again are those who were subbed for.