This is a standard feature of ERPNext that if user is entering data in a child table , it adds an empty line automatically for convenience in data entry. While this helpful in speeding up the data entry, the system should also keep track of those empty lines that either user has really entered the data on them or not and it not then remove those line automatically while saving the doc (Sales Order, Journal Entry and etc…) rather than giving the error to either enter the data on those line or must delete those line manually.
The above suggestion/enhancement is a standard feature in most popular ERPs and the demanding features of my client’s data entry users as you know that they need fast data entry systems and should not stop/slow them for unwanted actions.