A few times now I have went to mark off an invoice as complete to see it's already completed. Does the system sometimes automatically mark off invoices as complete?

Thanks for visiting the Community, @info827. To clarify, the invoice will automatically mark off as complete when the automation is checked in your Advance settings.

You can manage the automation setting at anytime. Here's how: 

1. In the Gear icon, select the Accounts and Settings. 
2. Go to Advanced. 
3. In the Automation section, deselect the Automatically apply credits if you want to automatically mark off invoices as complete. Otherwise, deselect that option to turn off this setting so it will un-applied payments or credits to open transactions. 

For your reference, read through this article: Configure Accounts and Setting. It includes steps to customize certain features in QuickBooks to help you manage your business easily. 

Let me know if you have more questions. We're always delighted to assist.