Hi Matt,
Are tickets being sent to orders in Pending status? If so, that’s a problem indeed, though one I could not replicate on my test site in default conditions.
As long as an order is set to Pending, there should be no way to immediately check that person in because (1) they have not received a ticket to use to check in at the door and (2) the system does not process those attendees as being able to be checked in.
For further clarification on that second point, here is a screenshot of the Attendee List in the WordPress admin that shows how the system both distinguishes Pending from Completed orders and prevents Pending orders from checking in:

If your team happens to be using the exported CSV file of attendees to check attendees in, it’s worth noting there is a column in there as well that indicates an attendee’s order is On Hold, which should also raise a red flag for checking them in manually offline.
Are you seeing something different on your site than what I’ve described so far? Please let me know because I’d be happy to look into this further if things are not working as they should be expected to.
Thanks,
Geoff