Hi Arun,
It's strange behavior and will not fall under SAP EM and it would be in SAP NW ABAP stack or Kernel Upgrade issue.
I just checked some OSS notes but I can find only match with your issue this SAP OSS note 1788514 - Authorization check when setting external breakpoints
or 2200135 - External breakpoint cannot be created
Update SAP NWABAP stack version in your SAP OSS message that will speed up the process to give you a solution.
Regards
GGOPII