Are the mobile users blocked from completing log in to Azure when this happens?
Do you also have any CA policies applied to mobile app sign-in with the “Require multifactor authentication” access control?
Azure does not recognize the Duo custom control for CA (or any third-party custom control) as “multifactor authentication”, so if you have a CA policy applied that includes the “Require multifactor authentication” rule, then it can’t be satisfied by third-party custom controls.
The information here describes Microsoft’s limitations for custom controls.