Incorrect administration of free throw (inadvertent horn)

[CJP]

A free thrower has the ball at his disposal. 1st of 2 shots. The score keeper inadvertently sounds the horn. A couple of seconds pass with no confusion on the players behalf. The shooter stayed focused on his shot and makes it. No whistle by any of the officials. The crew checks with the table. The crew looks absolutely confused. The administering official waves off the made free throw. In the end, the player made both (3 total) so no harm really. I am 99.999 percent sure it should have counted. Is there something I am missing where it is correct to not count this point?