inadvertent time out??

[vawils]

End of game situation (last minute) in a close game. B scores and A coach signals time out. I whistle and signal the time out but as I go towards the scorekeeper he claims he doesn't want a time out after the clock has been stopped. He then proceeds to try to substitute players. B players already huddling at their bench with their coach. I call them all back on the court but since the clock has now stopped the substitutes were allowed in. B also substitutes. Know we probably didn't handle this great and think the coach was just playing games to get his subs in. But once the clock is stopped we had to restart with a throw - in. Any thoughts on how this should have been handled differently. Charge A with a time out even when coach says doesn't want one?? Could've handled as an inadvertent whistle - can teams sub then?