Out then safe then out...

[Steven Tyler]

Sounds like the umpire put the runner in jeopardy with a case of horrible timing.

Put the runner back on 2B.

[tjones1]

Agree - put runner back on 2nd and play on.

[txump81]

I would agree with Steven. Since the umpire stopped play with the 3rd out, the runner should keep 2B. Like an inadvertent whistle or TIME call.

[MatthewPV]

Are there any rule references that I could use to argue that the ball is dead based on the fact it was the 3rd out?

[bob jenkins]

Originally Posted by MatthewPV

Are there any rule references that I could use to argue that the ball is dead based on the fact it was the 3rd out?

No. After all, the defense could still appeal another runner (in a different play) after the third out is made.

[MatthewPV]

So this would be "unprotestable" since the umpire didn't mess up a rule? Would there be anything anyone could to protest his actions?

[Rich Ives]

MLBUM 4.12

Umpire error.

Fix it.

If an umpire's error such as a missed count or number of outs clearly affects the play, every attempt should be made to correct the error, if possible.

Play: Runner on first base is stealing with a 3-1 count on the batter. The next pitch is called ball four, but the catcher throws the ball to second base anyway, and the runner is tagged before reaching the base. Umpire erroneously calls the runner out, and the runner, believing he is out,
steps off the bag and is again tagged by the fielder.

Ruling: The runner left second base under the assumption that the runner was out; however, the out was declared as a result of umpire error. In this situation the runner should be returned to second base. This is a correctable umpire error.

[BK47]

I agree, that is Umpire error which is correctable. Poor timing leads to this. I was once told this bit of advice "If you think your timing is to slow, Slow down some more."