Finally figured out a solid repro. Looks like it happens when an old version of the file is open in another pane, so when it tries to preview the file it first reloads it:
echo "asdf" > asdf.txt
echo "aoeu" > aoeu.txt
Layout > 2 Columns
Open aoeu.txt on the left, and asdf.txt on the right
Make sure the right pane is focussed
Go back to ST2, press Cmd+P (should show up on the right pane), and start typing aoeu. At some point the characters will fall through to the view.
From here you can undo your changes, close aoeu.txt on the right pane, and then touch again to repro again.