Hi asha,
System behavior is right. To run the RA for first level, you have to delete RA of second level.
For this follow it:
Delete RA of second level using T.code KKA8.
Then, Delete the Wbs-element If really need to delete other wise Teco it.
Now you can do RA for 1st level wbs-element.
I am sure it will work.
Try this.
Thanks
Rahul