"workflow was sent to one user(A) and when it did not take action on that , there was a background step which was supposed to fetch his manager(B) and send him.
problem occurred when background step which was supposed to fetch manager has user A as actual agent as per log and as only status was changed for work item , it did not fetch any manager and being next step a general task, it went to all users."
Looks like you will have to fix your agent determination rule here. Either error out in the method if no valid agent is found (WF Admin will work with others to fix master data/advise improvements in agent determination based on analysis and restart the workitem ) OR code a fall back agent who will be a person responsible to handle exceptions.
Regards
Sandy