I don't really understand the report or how to reproduce it.
It possibly looks like you've permanently deleted a thread and then the ID was reused. This is the sort of thing that you'd likely only see in a local development server as IDs won't be reused unless MySQL is restarted (and there is nothing higher than the ID in the DB). Obviously we need to maintain the thread's information and relationships across a hard delete, so changing this behavior is probably worse.