GST is not applying on some invoices even though it has been set up

Hi Inservio, 

Thank you for reaching out and welcome to our community!

So that we can better assist you with this, I would encourage you to get in touch with our support team so we can take a better look with you via a SmartLook (screen share) session. Please find their contact detail in this article: Get help with QuickBooks products and services.

Thank you and please let us know if you require any additional assistance.