Whilst working on ground handling at MAN, several years ago, we were informed that such a situation was impossible, due to the marvellous nature of modern check-in software.
Nice theory but the reality is that it can and does happen. It only takes one situation that hasn't been tested for by the developers actually occuring in live usage and the inevitable glitches will show up.
Nice to hear that you got to experience the joys of TK J for your troubles, so perhaps this cloud really did have a siver lining