@Jordan Fox Thank you for reaching out to us, Please help us with the below information which will help in troubleshooting this issue further,
- Have you enabled MFA for the user on the admin portal (Using per-user policy or Conditional access policy)
- Is this isolated to 1 user only?
- While registering on the Microsoft Authenticator application on his/her phone, did the user select Work account or personal account?
- could you also confirm if the user is trying to scan the QR code in the Microsoft Authenticator Application? (Add work or school account, followed by Scan QR code)?
- Is the user device able to scan any other QR Code.
- Can we also try out any other device for registering the same user for MFA ?
- Instead of scanning QR code, what happens if user enters code/url to register for MFA
Lets gather this information to isolate the issue further. If you have any further queries, please feel free to post back.