Substitution issue

[Sapper33]

NFHS, Varsity Boys game. Visiting team down 6 or 7 points. Under 2 minutes to go, Foul is called, home team shooting 2 frees, foul reported, I look at the C, he's ready to go, I'm ready to give ball to freethrower, T is talking to coach about foul (I assume)looking my way, Free thrower shoots 1st free and misses. While free thrower was shooting visiting team player runs onto the court and now there is confusion. What happened(C and myself did not know this) was that V team player had fouled out and they were replacing him and that was why V team player came out onto the court. Free throw should not have taken place. The 3 wise men get together and we determine that we will shoot both free throws since the first one should not have happened to begin with. Shooter makes both. Question is, did we make the right decision on wether to shoot both frees or should he only shoot the 2nd free? On a side note, I never saw the V team sub come onto the court and thats what I told my partners. Sorry for the long post. Hope it's not too confusing..