Welcome to the Microsoft Q&A Platform. Thank you for reaching out & I hope you are doing well.
I understand that you are experiencing more number of Health Probes from Azure Traffic Manager to Azure Application Gateway (added as a endpoint).
This is expected.
See : How endpoint monitoring works
Traffic Manager probes from multiple locations. The consecutive failure determines what happen within each region. That's why endpoints are receiving health probes from Traffic Manager with a higher frequency than the setting used for Probing Interval.
This is happening as probes are arriving from different locations (and each location follows the probe configuration i.e. Probe Interval)
Hope this helps.
Cheers,
Kapil.