Since, this is a lookup on 2 objects, whenever we try to search the user with this field, the system is trying to look after the users for the same and it is unable to fetch as it is a lookup on 2 objects and it is unable resolve the search results.
The SFDC has given a feasibility to select the uses from any of those 2 objects and hence this was handled in a different manner in SFDC and in our application app search is not working.
As a workaround, We have to create one additional field and create lookup for user object populate the data.
Please suggest a way to fix this permanently. Let me know if more information is required.