Baseball: If there standing on the same base are they out?

ok so today in my high school game there was a really crappy umpire and he was the absolute worst ump ive ever seen in my life but anyone he made tons of bad calls and one of them was when we had a fly ball and the person on first went to second and the person hitting it went to second and both of them were standing on second base so we threw the ball to second tagged them both he called both of them out we ran into the dough out when the other coach on the opposite team flipped out and was yelling what was the correct call and is it true that once you make a call you cant undo the call inless the player drops the ball?