Allow me lend a hand by providing some information about creating invoices in QuickBooks Online. When you use a subtotal to your transactions, it adds up all the items above it.
For example, if your sales invoice contains different types of item such as products and services, you can group them together. It allows you to provide customers detailed summary to the charges (please see screenshot below).
Now, if you no longer need to use subtotals, simple click the Clear all lines option. The button is visible beside Add subtotal.
Also, I encourage you provide some screenshots of the invoice so we can check the two different subtotals you're referring to.