6 players on the court - what would you do?

[Ref in PA]

This situation (or close to it) happened to me this weekend. Was doing two man in a 6th grade boys tournament and I was the trail about to administer a throwin in back court. Team A ran players to the table and so we subbed them in. Confusion sets in with boys going toward the bench, then back toward the court a couple of times. I make a quick count and have six As on the court. I whistle and tell the coach to get one off. More confusion. I see a kid go off and turn back to get ready for the throw in. I check my partner - he points back, we are ready to go - I administer the throw-in. We are halfway up the court and my partner blows the whistle - 6 As on the court. How I don't know. Partner called a team T on A. I still don't know how that happened. I was embarrassed - and I should have counted one last time, but the delay was already very long and I was ready for the game to continue. There is a lot to be said for taking your time