Late in the 4th quarter ball goes out of bound underneath the basket on the right side away from team A bench, team A than calls a time-out to set up a in bound play.

After the time-out player A1 is at the designated throw in spot where it should of been originaly, instead my p was on the opposite side and gave the ball to player A2 for the throw in at the spot closet to the bench now the ball is at the thrower disposal and player A1 is still out of bounds and than come back in when he realized that the throw in was on the other side,meanwhile team B coach is yelling that it is an violation for 2 players being out of bounds at the same time.
I have never herd of this rule can anyone help me on this ruling and what could have I done if that is true?

Yes, the B coach was right. It's a violation if 2 players of the same team are OOB when a spot throw-in begins. That's rule 9-2-12. If your partner didn't call it right away, it's too late to call it retroactively. The best thing that you could have done in this situation would have been to stop play immediately as soon as you noticed that your partner was setting up the throw-in at the wrong spot, and then re-set everything at the original spot. If you miss the violation, well, it's a learning process. Won't happen again, will it?