Did the offense give up their at bat?

[tskill]

This was a weird one... no outs long inning, home team at bat bottom of 3rd, R1 on 2nd, R2 on 1st. B3 hits into a nice 6-4-3, now 2outs and R1 on 3rd. The defense having a sudden boost of emotion after that nice double play runs off the field. The base coaches turn and with them head off the field, R1 heads off the field. The home team now starts taking its position in the field and pitcher steps on the mound. All along no one from either team has said anything about there only being 2 outs. And oddly enough a crowd that seemed to chirp the entire game didn't say anything either. Then as the pitcher starts with a warmup throw, the catcher turns and says to the home team coach, hey i think that was only 2 outs, then the score keeper tells the home coach they only have 2 outs.

A lot of particular rule instances I think could be applied here, but would like to see what the opinions are......

You're the UIC, What's the call under NFHS rules?