RichInSpirit, I wouldn't be too concerned by this phenomenon. For one thing, it is a regular occurrence and it regularly rights itself. I have never seen a ghost transaction hanging around. They have quite a bit of grist for their mill every night to run through, processing them all would take considerable amount of data manipulation, yet they get it right at the end. Chances are these are systems well-tested by repeated heavy usage, they may be fairly old in terms of design or build but replacing them with a newer system would actually do much more real damage.
Besides, the ghost transactions you see may not be artefacts of the database at all, they may not reflect true data but are actually ghosts generated by a reporting system trying to do something at the same time as a batch process is running updating hundreds of thousands of records.
As a general rule you try not to report and update at the same time because you can get false results in your report.