The controversy happened at the New Jersey Sports Interscholastic Athletic Association Group 2 semifinal game between the Camden Panthers and the Manasquan Warriors on Tuesday ... a matchup that came down to the wire.

The Panthers were up by 1 with just under 6 seconds left ... and after Warriors hooper Rey Weinseimer missed a 3-pointer, his teammate Griffin Linstra was positioned perfectly and nailed a put-back right before the clock hit zeros.

Warriors win, right?! That's what everyone in the gym thought ... but after a quick meeting, referees waived off the shot -- reversing the outcome.

The call was shocking, considering footage clearly shows time on the clock (.4 seconds) when the ball left Linstra's hand ... and the officials' mistake robbed the Warriors of advancing to the championship game.

The NJSIAA confirmed the refs were wrong ... but rejected Manasquan's appeal regardless, claiming they could not change the final score.

"So while the officiating crews' reports indicate that a post-game review of footage of the play in question convinced them that the basket should have counted, the results could not then and cannot now be changed," NJSIAA said.

"These are the rules of the game that all schools agree to follow, and which have been upheld on appeal. We apologize to the Manasquan team for the error."

The organization explained because the refs left the "visual confines of the playing court," the outcome was set in stone.

As you can imagine, Manasquan head coach Andrew Bilodeau was furious ... not only for his players -- but the Panthers as well.

"My heart for our kids but it also hurts for Camden. I hate to see their win be tarnished with any controversy. No kids deserve that."