I have asked around to get some ideas of a scenario that this could happen and the only possibility if the database was changed manually and then try to delete an option and since the database is modified manually the delete will actually not work correctly.
I would recommend that when you starting inserting the products, to create a mysql dump each time you add a certain number of products (20 - 50), so you will have a back up to go back to.
I'm not sure if you are planning to insert the products again, but i recommend that you clear the tables before doing that by running a truncate table command.
let me know if you have any other questions.