"You can't call that

[just another ref]

this late in the game." VB game tonight. Team A trailed by 8 to 12 most of the night but made a run in the last 2 minutes and got close. A turnover and a long 3 and we now have a 1 point game with less than 10 seconds to go. A is out of timeouts so B inbounds the ball, a long pass to midcourt followed by a foul with 00:01 showing on the clock. (old clock, no tenths) Here's where it gets interesting. Partner calls intentional foul. This foul took place right in front of A's bench, so now, after the free throws, we get to inbound the ball at the spot. Coach A now took a little swipe at my partner, something to the effect of "he doesn't even watch basketball on tv." I also heard the word sh*t in there somewhere, but I thought. ":01 and let's go home." A's 6'6" center stepped up to pressure the 6'0" guy taking the ball out. I waved my hand over the plane, as I usually do, handed the ball to B and stepped back. By the count of 3 A's big guy had stepped up and had both arms over the line above the elbow, hands almost out over B1's head. Bracing for the expected cries of "Mickey Mouse, etc." I blew the whistle and gave the warning. Instead, Coach A calmly said, "Yeah, that's right," and turned to direct his player, "straight up....don't reach over," or whatever. Give ball to B1, start to count, A1 stepped back up and did the exact same thing again. The last thing I wanted in this situation was a T, but I saw not much choice.
Thought Coach A was gonna cry. He kept saying over and over, "You don't call that this late in the game." So when do you call it? The more I think of it, I'm not even sure exactly what it was he meant. Maybe since it's only a second left that the call or lack thereof was meaningless anyway. But if that is the case, why would he not make his man back up.
Okay, let me hear from the important, knowledgeable people here. (you know who you are) Was what I did correct, unthinkable, or somewhere in between? As always, feed back is greatly appreciated.