Team A is ahead by two with 4 seconds left in game. Team A muffs an inbound pass the full length of court (ball untouched). Players make long walk back to inbound ball in front of Team B's bench under the basket. Players are pretty well matched up, partner on endline almost ready to inbound the ball. Team B had substituted but six remain on the court. I count and hold up six fingers hoping coach or partner would see. No luck. I jog over to partner as he is about to take final step to administer inbounds. I said six guys, he turned, no warning, and T'd Team B. Crowd and coach screaming he hadn't inbounded. We huddled, I said I was trying to get attention had to stop you, let's stay with T. Please advise, do we warn, or stay w/illegal sub?

There is no illegal sub, the replaced player simply hadn't left the floor. He has to get off the floor before you administer the FT. It's not a T until the ball becomes live. If you stopped him from administering the throw-in, then the ball isn't live. Get the 6th player off the floor and play ball.

In short, if the two of you didn't cancel the T, you screwed up.

Use your whistle to stop the play and your partner from admninistering the throw in rather than walk over. Then get the player off. No warning, no T and good game management. It almost sounds like your partner was looking for a reason rather than trying to be preventative.