Hello,
It sounds a like a potential configuration issue on the application within Duo, have you checked the informaation about limitations and best practices from Secure Access just to validate everything is properly configured https://securitydocs.cisco.com/docs/csa/olh/136532.dita the things I would highlight to be reviewed are:
- Secure Access supports provisioning a maximum of 1000 groups from Duo. Any groups beyond this number that are in scope are not provisioned. Secure Access does not restrict the number of users that you can provision from Duo. For more information, see Limitations and Range Limits.
- To ensure that all users are provisioned, assign the Everyone group to the Cisco Secure Access app. You can push other additional groups for group-based Secure Access rule enforcement.
- Duo does not support nested groups.
- If you previously imported groups from the on-premises AD and push the same groups from Duo, the groups from Duo do not overwrite the groups imported from the on-premises AD. You must reassign any group-based Secure Access policy rules to the groups imported from Duo.
The appropiate attribute mapping is very important as well https://securitydocs.cisco.com/docs/csa/olh/136568.dita:

Also, to review if there are any errors on some of the groups getting synced, could check the "Recent Logs" section withing the "Provisioning" tab whithin the Secure Access Provisioning App in Duo Dashboard.