What Did I Just See?

[NCAAREF]

OK, figure someone here will have an answer. NCAA Rules please. Watching the JV game before my contest last night and one of the JV officials calls a foul on a player. (2 shots to be awarded) The table informs him that is the 5th and DQ'ing foul so he walks towards his partner and informs him that #24 has 5 fouls. His partner then notifies #24 and he proceeds to leave the game. Now I know normally the non-calling official would notify the coach but in this case as quite often happens the calling official notified the coach of #24's fifth foul. No biggie so far. He then tells the table to time the 20 seconds for a sub. Now is when my eyes got BIG. While the one official is waiting for the DQ'd player to be replaced the other offical is administering the first FT. It missed, and now they have a coach who wants it reshot because he feels it should not have been administered until the sub was brought in, and the other coach who is saying what's the difference? It's the first of two. After the game they asked my and my partner what the correct proceedure was to get out of the the fix they put themselves in. Have to admit, I wasn't sure if there is an exact rule/reg to cover it and I'm still not. It wasn't an unmerited FT in my opinion so the whole correctable error thing is a mute point I think. Any suggestions?