@toijaz, I reviewed the entire thread from your September complaint. The common feature in the two topics is your reference to frequent opening of backups. You do not explain how you are doing this. But you need to understand that whenever you open a backup, it is converted to the data structure of the software version you use to open it. That backup cannot later be used by an older version of the program.
If you are importing all these backups, it would be very easy to confuse them in your list of businesses. If you are not importing them, but instead opening them directly, you must understand that changes made in one version do not carry over to another version. So I wonder if confusion over which version of the data file is in use has contributed to the problem.
Another possibility is that someone cloned a transaction, planning to modify it for a later sale, but lost track of which invoice was the original and which was the clone. Someone might have edited the original, believing it was the clone.
Whatever the source of the problem, it does not come from within the program. @lubos explained in the September thread why this cannot happen. Of course, no software program is 100% bug-free. But you are not describing a calculation error, incorrect allocation to an account, or similar problem. You are suggesting the ability of the program to magically add line items, change quantities, and record payments. The truth is, Manager has no capability to take any independent action. It responds only to inputs from users. When software updates occur, no new accounting data is added like you report. Existing data may be displayed differently, or additional reports might be available. But the program has no in-built intelligence that can meddle with your records. I promise you: if what you suggest were true, thousands of users would be complaining.
You mention “we” and putting the system “under deep scrutiny.” These remarks imply more than one person possibly has access. That is where you need to look to understand what is happening.