[Adam]

I disagree, but it might be based on how I am seeing the OP.
Foul called, and scorer tells the reporting official that it's a double-bonus shot. Clock keeper misses this and is still thinking one-and-one. Administering official tells the kids "two shots."
First shot goes up and misses, B1 gets the rebound in spite of ref's words and sprints the other way. Clock keeper meanwhile, already started the clock on the rebound because he thought it was live on a miss. Both refs take about two seconds to get their whistles in their mouths (it's the first of two, remember) and kill the play.
The refs didn't fail to award anything, the kids just didn't listen and the clock keeper was sleeping. Put the time back on and line 'm up.
What matters is what the administering official said; not whether or not time came off the clock. Now, if the refs ran down and set up with the new offense before realizing it, you're right. But it's not because time came off the clock.