Hello there, contact-gamingvi.

QuickBooks Online is dependent on the data transmitted by WooCommerce. 

I recommend contacting WooCommerce support if they have ways to prevent the free orders from importing into QuickBooks Online. Here's a link to contact their support: WooCommerce Community Support.

I'm also adding this that contains information about fixing errors you may encounter: Fix WooCommerce.

I'll be right here if you need more help.