This is may just be a bug in the pbp text. I have the league files, but since I've already left the game, I don't think you can revisit the pbp text. If I am wrong about that, let me know, and I'll send the files.
This is what happened:
---
Runner on first. Second base open. One out.
Runner on first tries to steal second.
Strike three called on the pitch (may have been swinging).
Catcher drops the pitch. Catcher picks it up and tags the batter. (this is the bug)
Catcher throws to second to try to get the runner.
---
The catcher did not have to tag the batter.
The dropped third strike rule (MLB 6.09(b)) stipulates that the batter becomes a runner on a dropped third strike if first base is not occupied or if there are two outs.
On this play, neither is true. Therefore the batter does not become a runner, and the catcher does not have to tag him.
It seems that OOTP may be (incorrectly) considering 1st base open if the runner on 1st attempted to steal on the pitch. The only definition I can find in the MLB rules of when a runner "occupies" a base is at the end of the comment after 7.08(b): "...A runner occupies a base until he legally acquires the next base."
Therefore the runner still occupies first base, and the batter is out as soon as strike three is called.
Research:
Official Rules | MLB.com: Official info
When is a base considered occupied?
3rd Strike Rule - timing for 1st being occupied? - Forums