Double Jeopardy?

Question
Last night at the ballpark in between my boy's ball games, there was an interesting play during the game I watched.  A batter had hit a ball that was caught, yet the batter went to first and was never told to go back to the dugout.  Umpires and scorekeepers had the batter down as out.  The next batter hits and the runner on first (who was already out) ran to second, but was thrown out at second before reaching the base safely.  What is the right call?  They charged the team with 2 outs for that one player.  Once on the fly ball and once on the out at second.

I look forward to hearing your response & I wonder if there has ever been a similar situation!  Thanks.

Answer
Hi Regina,

you're telling me a fly ball was caught for an out, and no umpire or coach noticed we had a runner on 1st??????   No I've never seen it.

What I have is a runner already out causing a throw by the defense, the runner closest to home is also out, if that's the b-r ok.  2 outs anyway you look at it.

Mark